Hi Perl Experts,

I'm new for perl. Thanks to give some time for my question.I have extract shared positions between two files and now I have one file like following. File is tab delimited

Chr1 position  QUAL GT_1 GT_2

1. chr1 478493    595   G/T  G/C
2. chr1 879243    700   A/T  A/A
3. chr2 889922    1300  C/C  C/C
4. chr2 1926372   300   T/A  T/A 
5. chr3  237474   500   G/C  C/C
6. chr3   575757  700   A/T  A/A
7. chr3 6666874   746   T/T  T/T

and so on

I like to extract list in new file when column 4 not match with coloumn 5 then it has to print complete row in new file. Another thing I want It also to calculate how many A/T converted to AA

Expected output
chr position QUAL GT_1 GT_1
1. chr1 478493    595   G/T  G/C
2. chr1 879243    700   A/T  A/A
3. chr3  237474   500   G/C  C/C
4. chr3   575757  700   A/T  A/A

Total number A/T conveted to A/A =2
Total number G/C converted to C/C =1

Edited 1 Year Ago by Dani: Formatting fixed

Are you looing for something like this?

#!/usr/bin/perl

use warnings;
use strict;
use autodie qw/open close/;

print "Enter input filename->";
chomp(my $ifilename = <STDIN>);

open(my $IFILE, "<", $ifilename);

while ( <$IFILE> )
{
    chomp;
    my @data = split(/\t+/, $_);
    print "@data\n" unless ( $data[3] eq $data[4] )#print this to another file
}

close($IFILE);

__END__

Edited 3 Years Ago by gerard4143

Hi,

You can do this:

#!/usr/bin/perl
use warnings;
use strict;

my %count_variable_converted;

chomp( my $title = <DATA> );

print $title,$/;
while (<DATA>) {
    next if /^$/;
    s/\s$//g;
    my @data = split /\s+?/, $_, 5;

    $count_variable_converted{'A/T'}{'A/A'}++
      if ( $data[3] eq 'A/T' and $data[4] eq 'A/A' );   

    $count_variable_converted{'G/C'}{'C/C'}++
      if ( $data[3] eq 'G/C' and $data[4] eq 'C/C' );

    if ( $data[3] ne $data[4] ) {
        print +( join "\t" => @data ), $/;
    }
}

for my $gt_1 ( keys %count_variable_converted ) {    
    for my $gt_2 ( keys %{ $count_variable_converted{$gt_1} } ) {    
        print sprintf "Total Number %s converted to %s is %d\n" => $gt_1,
          $gt_2, $count_variable_converted{$gt_1}->{$gt_2}, $/;
    }    
}

__DATA__
Chr1 position  QUAL    GT_1     GT_2

chr1    478493  595 G/T G/C
chr1    879243  700 A/T A/A
chr2    889922  1300    C/C C/C
chr2    1926372 300 T/A T/A 
chr3    237474  500 G/C C/C
chr3    575757  700 A/T A/A
chr3    6666874 746 T/T T/T

OUTPUT

Chr1 position  QUAL    GT_1     GT_2
chr1    478493  595    G/T      G/C
chr1    879243  700    A/T      A/A
chr3    237474  500    G/C      C/C
chr3    575757  700    A/T      A/A
Total Number A/T converted to A/A is 2
Total Number G/C converted to C/C is 1

Of course, you would need the function open if you are reading from a file. Hope this helps.

Edited 3 Years Ago by 2teez

Thanks @2teez and Gerand for your time for reply with code suggestion . I tried these codes. but it's printing all lines . I tried the follwoing code using file handlind open function. 

#!/usr/bin/perl
use warnings;
use strict;
my %count_variable_converted;
my $INFILE='./Sample_file.txt';
open (INPUT,"<$INFILE");
while (<INPUT>) {
 next if /^$/;
    s/\s$//g;
    my @data = split /\s+?/, $_, 5;
   $count_variable_converted{'A/T'}{'A/A'}++
    if ( $data[3] eq 'A/T' and $data[4] eq 'A/A' );

    $count_variable_converted{'G/C'}{'C/C'}++
      if ( $data[3] eq 'G/C' and $data[4] eq 'C/C' );
    if ( $data[3] ne $data[4] ) {

        print +( join "\t" => @data ), $/;
    }
}

for my $gt_1 ( keys %count_variable_converted ) {

   for my $gt_2 ( keys %{ $count_variable_converted{$gt_1} } ) {

        print sprintf "Total Number %s converted to %s is %d\n" => $gt_1,
          $gt_2, $count_variable_converted{$gt_1}->{$gt_2}, $/;
}
}

close INPUT;

The output of this code looks like this . When data[3] and data[4] equal. It shows two errors.It also did not count.

Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 1.
CHR     POS     GT_1    GT_2
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 2.
chr1    12354   A/T     A/A
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 3.
chr1    43554   G/C     C/C
Use of uninitialized value $data[4] in string eq at ./Count.pl line 14, <INPUT> line 4.
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 4.
chr1    76767   G/C     G/C
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 5.
chr2    42525   A/T     A/A
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 5.
chr2    76447   G/C     C/C
Use of uninitialized value $data[4] in string eq at ./Mutation_Count.pl line 14, <INPUT> line 6.
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 6.
chr2    84332   G/C     G/C
Use of uninitialized value in string ne at ./Count.pl line 16, <INPUT> line 7.
chr3    34364   A/T     A/A

Edited 3 Years Ago by yksrmc

Hi,
I think the issue is with your file simple_file.txt. The code I gave should work perfectly.
However, I have attached to this mail, a sample of the file I used. Again see a modification of the code above.

#!/usr/bin/perl
use warnings;
use strict;

my %count_variable_converted;

my $filename = 'simple_file.txt';

open my $fh, '<', $filename or die "can't open file: $!";

chomp( my $title = <$fh> );

print $title, $/;
while (<$fh>) {
    next if /^$/;

    my @data = ( $1, $2, $3, $4, $5 )
      if m/^     # start from the beginning of the each line
          (.+?)  # $1
           \s+?  # space or tab
           (.+?) # $2
           \s+?  # space or tab
           (.+?) # $3
           \s+?  # space or tab
           (.+?) # $4
           \s+?  # space or tab
           (.+?) # $5
           $     # end of the line
         /x;

    $count_variable_converted{'A/T'}{'A/A'}++
      if ( $data[3] eq 'A/T' and $data[4] eq 'A/A' );

    $count_variable_converted{'G/C'}{'C/C'}++
      if ( $data[3] eq 'G/C' and $data[4] eq 'C/C' );

    if ( $data[3] ne $data[4] ) {
        print +( join "\t" => @data ), $/;
    }
}

close $fh or die "can't close file: $!";

for my $gt_1 ( keys %count_variable_converted ) {
    for my $gt_2 ( keys %{ $count_variable_converted{$gt_1} } ) {
        print sprintf "Total Number %s converted to %s is %d\n" => $gt_1,
          $gt_2, $count_variable_converted{$gt_1}->{$gt_2}, $/;
    }
}

Using regexp to pick out the values needed for each line. Please do let us know if this works for you.

I went throught your code and there are a number of old or wrong ways of doing perl.

  1. Always check the return of the open function using perl , also for close function. Or you use autodie has shown by gerard4143.
  2. Use 3 arugment option of open function
  3. use lexically scope file-handles in open function.
Attachments
Chr1 position  QUAL    GT_1     GT_2

chr1	478493	595	G/T	G/C
chr1	879243	700	A/T	A/A
chr2	889922	1300	C/C	C/C
chr2	1926372	300	T/A	T/A 
chr3	237474	500	G/C	C/C
chr3	575757	700	A/T	A/A
chr3	6666874	746	T/T	T/T
Thanks 2teez.!! Yes you are right, your code is working perfect. However It has one some bugs which I noticed. It prints those lines too which satisfy just one condition only either G/C or C/C. It's not printing only those lines which satisfy both conditions. It's checking one condition. it print reverse combition line too like Gt_1 CC and Gt_2  G/C

Like It prints those lines too which has just either  for example our condition is 'G/C' and 'C/C'. So it should print print those lines which has cloumn GT1 as G/C and Column GT_2 as C/C

It printing following combinations too.

GT_1   GT_2
 C/C    G/C
 T/C    C/C
 C/C    T/C
 C/C    C/C

 Thanks Counting work doing perfect. It's counting only those lines which satisfy both conditions. I just like to know why on printing it's printing all lines which satisfy just one condition. I hope you got my point. BTW thanks for all your reply. Before to close this question. It 'll be great pleasure if this bug of checking one condition for printing could sort out too.

Thanks I have got the reason why for printing all lines are printing, because for printing we used condition data[3] ne data[4]. So it would print all lines which are mismatch with any combination. .I'll mark as question solved in couple of days Thanks 2teez and Gerard for your time and prompt reply.

Edited 3 Years Ago by yksrmc

Hi,

However It has one some bugs which I noticed.

No, it hasn't. The script I wrote address the original condition you gave:

I like to extract list in new file when column 4 not match with coloumn 5

So, as long as column 4 is NOT equal to column 5, that whole line is printed and since 'C/C' is not equal 'G/C' the line is also printed.

Thanks 2teez, That's why at last I mentioned I got the reason why those lines are also printing. I got your point. I have marked question as solved.

Edited 1 Year Ago by Dani: Formatting fixed. Only indent code please.

Hi yksrmc,

Majorly I think it all has to do with your input data. Below is another solution, using map function and hash value. Of course it's fewer lines compare to the ones before. It also give a correct output considering the new condition you gave.

#!/usr/bin/perl
use warnings;
use strict;
use constant TITLE => "Chr1 position  QUAL    GT_1     GT_2
";

<DATA> for 1 .. 2;    ## ignore the first two lines

my $counter = {};

print TITLE;
print join "\t" => map {
    $_->[4] =~ s/^\s+|\s+$//g;
    $counter->{'A/T'}{'A/A'}++ if $_->[3] eq 'A/T' and $_->[4] eq 'A/A';
    $counter->{'G/C'}{'C/C'}++ if $_->[3] eq 'G/C' and $_->[4] eq 'C/C';

    @$_, $/ if $_->[3] ne $_->[4] and $_->[3] ne ( 'C/C' or 'A/A' );
}[ ( split /\s+/, $_, 5 )[ 0 .. 4 ] ] while <DATA>;

print map {
    sprintf "The Total Number of %s converted to %s is %d\n",
      $_, %{ $counter->{$_} }
} keys %$counter;

__DATA__
Chr1 position  QUAL    GT_1     GT_2

chr1    478493  595 G/T G/C
chr1    879243  700 A/T A/A
chr2    889922  1300    C/C C/C
chr2    1926372 300 T/A T/A 
chr3    237474  500 G/C C/C
chr3    575757  700 A/T A/A
chr3    6666874 746 T/T T/T
chr3    6666874 746 C/C G/C

Thanks Gerard and 2teez for your time, but I tried all suggested code but . It prints all the lines which are like coloumn3 AA and column 4 AA. When I try it on real data, It's printing everything condition match or not. Could you help to sort out. I have attached data file, I don't know the reason when we have given condition then why It's printing everything. Could you try why what's wrong with code for following data.

Edited 1 Year Ago by Dani: Formatting fixed

Attachments
391440	chr19	261481	112.04	T/C	C/C
391441	chr19	267952	35.77	C/C	C/C
391442	chr19	267955	35.77	G/G	G/G
391445	chr19	297327	74.02	A/G	A/G
391446	chr19	297336	339	T/T	G/T
391447	chr19	297402	303	C/C	C/C
391448	chr19	297453	234.01	T/A	T/A
391449	chr19	297456	203.01	A/G	A/G
391451	chr19	297509	90.51	T/T	T/T
391452	chr19	297519	83.51	G/G	G/G
391453	chr19	297612	35.77	A/A	A/A
391454	chr19	297652	147.01	C/T	C/T
391456	chr19	298004	89.04	A/G	G/G
391457	chr19	298005	89.04	T/A	A/A
391458	chr19	298008	89.04	A/G	G/G
391462	chr19	317203	150.26	A/A	G/A
391463	chr19	318308	198.06	C/C	C/C
391466	chr19	318853	335.01	C/G	C/G
391468	chr19	319157	83.01	T/A	T/A
391469	chr19	319159	80.01	T/C	T/C
391470	chr19	329854	1747	G/G	G/G
391471	chr19	329856	1747	G/G	G/G
391472	chr19	330307	195.01	A/G	A/G
391475	chr19	330342	605.01	T/C	T/C
391476	chr19	330539	116.01	C/T	C/T
391478	chr19	331028	1008	A/A	A/A
391479	chr19	331113	34.01	T/C	T/C
391480	chr19	331124	933	C/C	T/C
391481	chr19	331155	857	A/A	A/A
391484	chr19	355550	83.97	C/C	C/C
391485	chr19	355553	83.97	G/G	G/G
391486	chr19	356745	95.01	A/T	A/T
391487	chr19	356952	447.01	T/G	T/G
391488	chr19	356956	243.01	T/C	T/C
391489	chr19	356959	108.01	A/T	A/T
391490	chr19	356960	222.01	A/C	A/C
391491	chr19	356965	212.01	A/G	A/G
391494	chr19	365936	325	A/A	A/A
391495	chr19	365939	325	G/G	G/G
391497	chr19	414409	174.13	C/C	C/C
391498	chr19	470450	83.01	G/A	G/A
391499	chr19	470471	116.01	G/A	G/A
391507	chr19	503282	224.06	G/G	G/G
391508	chr19	503447	67.97	G/G	G/G
391509	chr19	503566	109.01	A/G	A/G
391512	chr19	521705	89.04	A/G	G/G
391513	chr19	521707	89.04	G/T	T/T
391516	chr19	522279	152.26	T/T	A/T
391517	chr19	522372	36.01	T/G	T/G
391525	chr19	552060	173.14	A/T	T/T
391526	chr19	552078	45.01	C/T	C/T
391528	chr19	552231	282.01	T/T	T/T
391529	chr19	552297	67.97	G/G	G/G
391530	chr19	552317	129.01	A/T	A/T
391536	chr19	553080	35.77	A/A	A/A
391537	chr19	553116	35.77	G/G	C/G
391538	chr19	553140	74.01	G/C	G/C
391539	chr19	553185	295	A/A	G/A
391540	chr19	553208	316.21	C/C	C/C
391541	chr19	553216	261.68	T/T	T/T
391543	chr19	553364	129.01	A/G	A/G
391545	chr19	553498	2536.01	C/G	C/G
391547	chr19	560551	35.77	T/T	G/T
391548	chr19	560598	49.01	A/G	A/G
391549	chr19	560603	49.01	T/C	T/C
391550	chr19	561019	173.01	G/C	G/C
391551	chr19	561068	55.01	A/T	A/T
391554	chr19	562074	395	G/G	G/G
391560	chr19	562134	602.01	A/C	C/C
391561	chr19	562184	1079	C/C	C/C
391562	chr19	562237	1126	A/A	A/A
391563	chr19	562292	558	G/G	G/G
391564	chr19	562530	410	C/C	C/C
391565	chr19	562840	1509.01	A/G	A/G
391569	chr19	636141	33.01	C/T	T/T
391571	chr19	636395	109.51	A/A	A/A
391572	chr19	654630	803	G/G	G/G
391574	chr19	654699	74.01	T/G	T/G
391575	chr19	654716	175.01	T/C	T/C
391576	chr19	654717	163.01	G/A	G/A
391579	chr19	654755	782.01	C/T	C/T
391580	chr19	654762	872.01	T/A	T/A
391583	chr19	654954	577.01	T/C	T/C
391584	chr19	654965	659.01	A/C	A/C
391585	chr19	655088	55.01	C/T	C/T
391586	chr19	655105	1619.01	C/A	C/A
391587	chr19	655107	1672.01	T/C	T/C
391588	chr19	655252	1831	G/G	G/G
391589	chr19	655253	1828	T/T	T/T
391590	chr19	656443	116.51	C/C	C/C
391591	chr19	656449	116.51	A/A	A/A
391594	chr19	669853	649	T/T	T/T
391595	chr19	669960	724	A/A	A/A
391599	chr19	684246	101.51	G/G	A/G
391600	chr19	684251	101.51	T/T	C/T
391601	chr19	684254	101.51	G/G	G/G
391609	chr19	697805	91.97	G/G	G/G
391611	chr19	698488	57.01	G/A	G/A
391612	chr19	698594	44.01	G/A	G/A
391615	chr19	699004	30.01	C/T	C/T
391616	chr19	700845	4662.01	G/G	G/G
391617	chr19	700864	6328.01	C/C	C/C
391618	chr19	701016	6232.01	C/C	C/C
391619	chr19	701187	113.01	T/C	C/C
391624	chr19	712242	1213	C/C	C/C
391625	chr19	712245	1236	T/T	T/T
391626	chr19	712340	417.01	T/C	T/C
391627	chr19	712351	389.01	C/T	C/T
391628	chr19	712410	1131.01	A/G	G/G
391629	chr19	712417	1185.01	T/C	T/C
391630	chr19	712896	95.01	A/G	A/G
391631	chr19	712898	93.01	A/T	A/T
391633	chr19	713804	284.01	A/T	A/T
391634	chr19	713811	278.01	G/A	G/A
391635	chr19	713912	171.01	T/C	T/C
391636	chr19	713916	171.01	T/C	T/C
391637	chr19	713928	358	G/G	G/G
391638	chr19	715765	35.77	C/C	C/C
391640	chr19	716199	41.76	G/G	G/G
391641	chr19	716207	34.12	T/A	A/A
391642	chr19	721818	339.01	A/G	A/G
391643	chr19	721820	337.01	A/T	A/T
391646	chr19	733976	370	G/G	G/G
391647	chr19	733982	370	G/G	G/G
391648	chr19	734292	69.01	C/G	C/G
391650	chr19	734304	95.01	G/A	G/A
391652	chr19	734626	32.01	C/A	C/A
391653	chr19	734641	1232	A/A	A/A
391654	chr19	734644	1215	G/G	G/G
391656	chr19	737041	132.51	G/G	G/G
391658	chr19	738200	49.01	G/A	G/A
391659	chr19	744395	101.51	G/G	G/G
391660	chr19	744501	101.51	C/C	C/C
391661	chr19	744671	97.01	C/A	C/A
391662	chr19	744689	244.01	T/A	T/A
391663	chr19	744880	323.46	C/T	G/C
391664	chr19	745170	307.01	A/G	A/G
391665	chr19	745176	342.01	A/G	A/G
391666	chr19	745438	56.01	C/A	C/A
391668	chr19	745489	224.01	T/A	T/A
391669	chr19	745491	331.01	T/C	T/C
391670	chr19	745675	375.76	A/A	G/A
391673	chr19	754610	253.01	C/G	G/G
391674	chr19	754621	455.01	T/C	C/C
391675	chr19	755679	98.01	T/C	T/C
391677	chr19	755719	486	G/G	G/G
391680	chr19	759242	742	C/C	C/C
391681	chr19	759245	770	T/T	T/T
391682	chr19	759422	971	C/C	C/C
391683	chr19	759615	103.01	C/T	T/T
391686	chr19	760397	54.01	A/G	A/G
391689	chr19	769425	85.97	G/G	G/G
391690	chr19	769610	72.01	A/G	A/G
391691	chr19	770052	89.01	C/T	C/T
391693	chr19	770092	395.01	A/G	G/G
391694	chr19	770640	231.01	A/G	A/G
391696	chr19	776398	148.26	G/G	G/G
391699	chr19	777239	91.01	G/A	G/A
391700	chr19	777295	213.06	G/G	A/G
391701	chr19	777306	213.06	A/A	T/A
391702	chr19	818999	43.76	C/C	C/C
391703	chr19	823114	173.26	C/C	C/C
391709	chr19	849222	796	T/T	T/T
391712	chr19	864868	43.76	A/A	A/A
391713	chr19	864889	43.76	C/C	T/C
391718	chr19	905287	43.76	A/A	A/A
391719	chr19	905292	43.76	A/A	A/A
391721	chr19	914264	834	G/G	G/G
391722	chr19	914382	467.01	T/A	T/A
391723	chr19	914384	467.01	T/C	T/C
391724	chr19	914429	77.01	C/A	C/A
391725	chr19	914687	83.97	C/C	C/C
391726	chr19	914689	83.97	A/A	A/A
391730	chr19	958384	30.77	T/T	T/T
391731	chr19	958423	2755	G/G	G/G
391732	chr19	958631	126.01	C/T	C/T
391733	chr19	958659	204.01	C/T	C/T
391734	chr19	958660	110.01	G/A	G/A
391735	chr19	958664	296.01	C/T	C/T
391736	chr19	958665	236.01	G/A	G/A
391737	chr19	958668	311.01	C/T	C/T
391738	chr19	958669	109.01	G/A	G/A
391741	chr19	966155	299.77	T/C	T/C
391742	chr19	966255	155.01	T/A	T/A
391743	chr19	966258	144.01	A/G	A/G
391745	chr19	966445	332.01	T/C	T/C
391746	chr19	966448	394.01	A/G	A/G
391748	chr19	967021	391.01	A/G	A/G
391749	chr19	967053	562.01	T/A	T/A
391750	chr19	967060	501.01	T/C	T/C
391753	chr19	967584	101.51	C/C	C/C
391754	chr19	967917	250.01	T/C	T/C
391755	chr19	968031	470.01	T/C	T/C
391756	chr19	968150	391.06	A/G	G/G
391758	chr19	1025134	43.76	A/A	G/A
391759	chr19	1025136	43.76	A/A	T/A
391760	chr19	1059486	382	G/G	G/G
391762	chr19	1059555	37.01	C/T	C/T
391763	chr19	1061377	67.97	G/G	G/G
391764	chr19	1061380	67.97	A/A	A/A
391765	chr19	1061478	67.97	G/G	G/G
391766	chr19	1061485	67.97	G/G	G/G
391767	chr19	1076718	211.27	A/T	A/T
391768	chr19	1078173	127.07	T/C	C/C
391771	chr19	1100930	49.76	C/C	C/C
391772	chr19	1100976	47.76	C/C	C/C
391773	chr19	1120472	101.51	C/C	C/C
391774	chr19	1120480	101.51	C/C	C/C
391775	chr19	1120493	101.51	A/A	A/A
391776	chr19	1120495	101.51	T/T	T/T
391777	chr19	1120503	101.51	T/T	T/T
391778	chr19	1120514	101.51	A/A	A/A
391779	chr19	1120693	119.07	A/G	G/G
391780	chr19	1142761	2474	A/A	A/A
391781	chr19	1142786	35.77	T/T	C/T
391783	chr19	1176955	162.13	C/C	T/C
391784	chr19	1176963	134.26	C/C	T/C
391787	chr19	1178741	1381	T/T	T/T
391788	chr19	1178745	1461	C/C	C/C
391789	chr19	1178768	128.01	T/C	T/C
391790	chr19	1184956	678	G/G	G/G
391791	chr19	1184964	678	G/G	G/G
391792	chr19	1185312	86.01	T/A	T/A
391793	chr19	1185314	86.01	T/C	T/C
391794	chr19	1188756	80.01	T/C	T/C
391795	chr19	1188829	109.02	A/G	A/G
391797	chr19	1188908	431.01	A/T	A/T
391801	chr19	1189225	124.01	A/T	A/T
391802	chr19	1189232	161.01	G/A	G/A
391803	chr19	1189814	463	C/C	T/C
391807	chr19	1194065	134.26	T/T	C/T
391808	chr19	1194158	134.26	A/A	G/A
391809	chr19	1194167	134.26	C/C	T/C
391810	chr19	1201542	305.01	C/C	C/C
391812	chr19	1212756	58.02	T/G	T/G
391814	chr19	1212778	577.23	T/C	A/C
391815	chr19	1213018	703	C/C	C/C
391816	chr19	1306280	179.13	T/T	T/T
391817	chr19	1306579	31.02	T/C	T/C
391818	chr19	1306837	437	C/C	C/C
391819	chr19	1319693	41.76	T/T	T/T
391820	chr19	1319993	234.03	T/T	A/T
391822	chr19	1320656	155.01	A/T	A/T
391823	chr19	1320657	193.01	T/C	T/C
391826	chr19	1320991	112.04	A/G	G/G
391828	chr19	1329002	345.76	C/C	C/C
391833	chr19	1329919	1177	T/T	A/T
391835	chr19	1330168	744	C/C	C/C
391836	chr19	1330984	56.97	A/A	C/A
391837	chr19	1335177	977.01	A/T	A/T
391838	chr19	1335224	160.01	A/G	A/G
391839	chr19	1335295	958.01	A/T	A/T
391840	chr19	1335615	2234	C/C	C/C
391841	chr19	1335638	67.97	G/G	A/G
391845	chr19	1341831	301	G/G	G/G
391846	chr19	1341839	241.98	A/G	G/G
391847	chr19	1341932	116.01	T/A	T/A
391848	chr19	1341945	213.01	A/G	A/G
391852	chr19	1342450	84.01	T/A	T/A
391853	chr19	1342499	75.01	G/A	G/A
391855	chr19	1342747	1100	A/A	A/A
391856	chr19	1342750	1010.01	G/G	A/G
391858	chr19	1342760	147.01	C/T	C/T
391867	chr19	1346232	52.01	T/C	T/C
391869	chr19	1346238	323.01	G/T	G/T
391870	chr19	1346247	512.22	A/T	A/T
391871	chr19	1346352	606.01	A/G	A/G
391873	chr19	1346548	386.01	G/C	G/C
391874	chr19	1346574	148.01	A/G	A/G
391875	chr19	1346596	217.01	A/G	A/G
391876	chr19	1346607	110.01	T/G	T/G
391877	chr19	1346616	153.01	A/C	A/T
391880	chr19	1346878	567	C/C	C/C
391881	chr19	1346884	567	C/C	C/C
391882	chr19	1347518	207.13	C/C	C/C
391884	chr19	1485568	135.51	G/G	A/G
391885	chr19	1485671	43.01	T/C	C/C
391889	chr19	1545304	101.51	G/G	G/G
391890	chr19	1545413	101.51	A/A	A/A
391893	chr19	1562510	565.01	T/C	T/C
391894	chr19	1562520	596.01	C/T	C/T
391896	chr19	1562818	248.06	A/A	A/A
391900	chr19	1586910	61.01	T/C	C/C
391902	chr19	1586983	137.26	G/G	G/G
391903	chr19	1594228	109.51	C/C	C/C
391904	chr19	1594233	66.02	A/T	T/T
391905	chr19	1594859	108.51	C/C	C/C
391906	chr19	1601151	15

Thanks Gerard and 2teez for your time, but I tried all suggested code but . It prints all the lines which are like coloumn3 AA and column 4 AA. When I try it on real data, It's printing everything condition match or not. Could you help to sort out. I have attached data file, I don't know the reason when we have given condition then why It's printing everything. Could you try why what's wrong with code for following data.

I have attached small real sample file. In this sample for example condition can be A/G to GG because other cases may be very rare. First column is serial number column

Could we apply for each or for loop for this problem to count condition

Thanks for your time for my query

Edited 3 Years Ago by yksrmc

Attachments
391440	chr19	261481	112.04	T/C	C/C
391441	chr19	267952	35.77	C/C	C/C
391442	chr19	267955	35.77	G/G	G/G
391445	chr19	297327	74.02	A/G	A/G
391446	chr19	297336	339	T/T	G/T
391447	chr19	297402	303	C/C	C/C
391448	chr19	297453	234.01	T/A	T/A
391449	chr19	297456	203.01	A/G	A/G
391451	chr19	297509	90.51	T/T	T/T
391452	chr19	297519	83.51	G/G	G/G
391453	chr19	297612	35.77	A/A	A/A
391454	chr19	297652	147.01	C/T	C/T
391456	chr19	298004	89.04	A/G	G/G
391457	chr19	298005	89.04	T/A	A/A
391458	chr19	298008	89.04	A/G	G/G
391462	chr19	317203	150.26	A/A	G/A
391463	chr19	318308	198.06	C/C	C/C
391466	chr19	318853	335.01	C/G	C/G
391468	chr19	319157	83.01	T/A	T/A
391469	chr19	319159	80.01	T/C	T/C
391470	chr19	329854	1747	G/G	G/G
391471	chr19	329856	1747	G/G	G/G
391472	chr19	330307	195.01	A/G	A/G
391475	chr19	330342	605.01	T/C	T/C
391476	chr19	330539	116.01	C/T	C/T
391478	chr19	331028	1008	A/A	A/A
391479	chr19	331113	34.01	T/C	T/C
391480	chr19	331124	933	C/C	T/C
391481	chr19	331155	857	A/A	A/A
391484	chr19	355550	83.97	C/C	C/C
391485	chr19	355553	83.97	G/G	G/G
391486	chr19	356745	95.01	A/T	A/T
391487	chr19	356952	447.01	T/G	T/G
391488	chr19	356956	243.01	T/C	T/C
391489	chr19	356959	108.01	A/T	A/T
391490	chr19	356960	222.01	A/C	A/C
391491	chr19	356965	212.01	A/G	A/G
391494	chr19	365936	325	A/A	A/A
391495	chr19	365939	325	G/G	G/G
391497	chr19	414409	174.13	C/C	C/C
391498	chr19	470450	83.01	G/A	G/A
391499	chr19	470471	116.01	G/A	G/A
391507	chr19	503282	224.06	G/G	G/G
391508	chr19	503447	67.97	G/G	G/G
391509	chr19	503566	109.01	A/G	A/G
391512	chr19	521705	89.04	A/G	G/G
391513	chr19	521707	89.04	G/T	T/T
391516	chr19	522279	152.26	T/T	A/T
391517	chr19	522372	36.01	T/G	T/G
391525	chr19	552060	173.14	A/T	T/T
391526	chr19	552078	45.01	C/T	C/T
391528	chr19	552231	282.01	T/T	T/T
391529	chr19	552297	67.97	G/G	G/G
391530	chr19	552317	129.01	A/T	A/T
391536	chr19	553080	35.77	A/A	A/A
391537	chr19	553116	35.77	G/G	C/G
391538	chr19	553140	74.01	G/C	G/C
391539	chr19	553185	295	A/A	G/A
391540	chr19	553208	316.21	C/C	C/C
391541	chr19	553216	261.68	T/T	T/T
391543	chr19	553364	129.01	A/G	A/G
391545	chr19	553498	2536.01	C/G	C/G
391547	chr19	560551	35.77	T/T	G/T
391548	chr19	560598	49.01	A/G	A/G
391549	chr19	560603	49.01	T/C	T/C
391550	chr19	561019	173.01	G/C	G/C
391551	chr19	561068	55.01	A/T	A/T
391554	chr19	562074	395	G/G	G/G
391560	chr19	562134	602.01	A/C	C/C
391561	chr19	562184	1079	C/C	C/C
391562	chr19	562237	1126	A/A	A/A
391563	chr19	562292	558	G/G	G/G
391564	chr19	562530	410	C/C	C/C
391565	chr19	562840	1509.01	A/G	A/G
391569	chr19	636141	33.01	C/T	T/T
391571	chr19	636395	109.51	A/A	A/A
391572	chr19	654630	803	G/G	G/G
391574	chr19	654699	74.01	T/G	T/G
391575	chr19	654716	175.01	T/C	T/C
391576	chr19	654717	163.01	G/A	G/A
391579	chr19	654755	782.01	C/T	C/T
391580	chr19	654762	872.01	T/A	T/A
391583	chr19	654954	577.01	T/C	T/C
391584	chr19	654965	659.01	A/C	A/C
391585	chr19	655088	55.01	C/T	C/T
391586	chr19	655105	1619.01	C/A	C/A
391587	chr19	655107	1672.01	T/C	T/C
391588	chr19	655252	1831	G/G	G/G
391589	chr19	655253	1828	T/T	T/T
391590	chr19	656443	116.51	C/C	C/C
391591	chr19	656449	116.51	A/A	A/A
391594	chr19	669853	649	T/T	T/T
391595	chr19	669960	724	A/A	A/A
391599	chr19	684246	101.51	G/G	A/G
391600	chr19	684251	101.51	T/T	C/T
391601	chr19	684254	101.51	G/G	G/G
391609	chr19	697805	91.97	G/G	G/G
391611	chr19	698488	57.01	G/A	G/A
391612	chr19	698594	44.01	G/A	G/A
391615	chr19	699004	30.01	C/T	C/T
391616	chr19	700845	4662.01	G/G	G/G
391617	chr19	700864	6328.01	C/C	C/C
391618	chr19	701016	6232.01	C/C	C/C
391619	chr19	701187	113.01	T/C	C/C
391624	chr19	712242	1213	C/C	C/C
391625	chr19	712245	1236	T/T	T/T
391626	chr19	712340	417.01	T/C	T/C
391627	chr19	712351	389.01	C/T	C/T
391628	chr19	712410	1131.01	A/G	G/G
391629	chr19	712417	1185.01	T/C	T/C
391630	chr19	712896	95.01	A/G	A/G
391631	chr19	712898	93.01	A/T	A/T
391633	chr19	713804	284.01	A/T	A/T
391634	chr19	713811	278.01	G/A	G/A
391635	chr19	713912	171.01	T/C	T/C
391636	chr19	713916	171.01	T/C	T/C
391637	chr19	713928	358	G/G	G/G
391638	chr19	715765	35.77	C/C	C/C
391640	chr19	716199	41.76	G/G	G/G
391641	chr19	716207	34.12	T/A	A/A
391642	chr19	721818	339.01	A/G	A/G
391643	chr19	721820	337.01	A/T	A/T
391646	chr19	733976	370	G/G	G/G
391647	chr19	733982	370	G/G	G/G
391648	chr19	734292	69.01	C/G	C/G
391650	chr19	734304	95.01	G/A	G/A
391652	chr19	734626	32.01	C/A	C/A
391653	chr19	734641	1232	A/A	A/A
391654	chr19	734644	1215	G/G	G/G
391656	chr19	737041	132.51	G/G	G/G
391658	chr19	738200	49.01	G/A	G/A
391659	chr19	744395	101.51	G/G	G/G
391660	chr19	744501	101.51	C/C	C/C
391661	chr19	744671	97.01	C/A	C/A
391662	chr19	744689	244.01	T/A	T/A
391663	chr19	744880	323.46	C/T	G/C
391664	chr19	745170	307.01	A/G	A/G
391665	chr19	745176	342.01	A/G	A/G
391666	chr19	745438	56.01	C/A	C/A
391668	chr19	745489	224.01	T/A	T/A
391669	chr19	745491	331.01	T/C	T/C
391670	chr19	745675	375.76	A/A	G/A
391673	chr19	754610	253.01	C/G	G/G
391674	chr19	754621	455.01	T/C	C/C
391675	chr19	755679	98.01	T/C	T/C
391677	chr19	755719	486	G/G	G/G
391680	chr19	759242	742	C/C	C/C
391681	chr19	759245	770	T/T	T/T
391682	chr19	759422	971	C/C	C/C
391683	chr19	759615	103.01	C/T	T/T
391686	chr19	760397	54.01	A/G	A/G
391689	chr19	769425	85.97	G/G	G/G
391690	chr19	769610	72.01	A/G	A/G
391691	chr19	770052	89.01	C/T	C/T
391693	chr19	770092	395.01	A/G	G/G
391694	chr19	770640	231.01	A/G	A/G
391696	chr19	776398	148.26	G/G	G/G
391699	chr19	777239	91.01	G/A	G/A
391700	chr19	777295	213.06	G/G	A/G
391701	chr19	777306	213.06	A/A	T/A
391702	chr19	818999	43.76	C/C	C/C
391703	chr19	823114	173.26	C/C	C/C
391709	chr19	849222	796	T/T	T/T
391712	chr19	864868	43.76	A/A	A/A
391713	chr19	864889	43.76	C/C	T/C
391718	chr19	905287	43.76	A/A	A/A
391719	chr19	905292	43.76	A/A	A/A
391721	chr19	914264	834	G/G	G/G
391722	chr19	914382	467.01	T/A	T/A
391723	chr19	914384	467.01	T/C	T/C
391724	chr19	914429	77.01	C/A	C/A
391725	chr19	914687	83.97	C/C	C/C
391726	chr19	914689	83.97	A/A	A/A
391730	chr19	958384	30.77	T/T	T/T
391731	chr19	958423	2755	G/G	G/G
391732	chr19	958631	126.01	C/T	C/T
391733	chr19	958659	204.01	C/T	C/T
391734	chr19	958660	110.01	G/A	G/A
391735	chr19	958664	296.01	C/T	C/T
391736	chr19	958665	236.01	G/A	G/A
391737	chr19	958668	311.01	C/T	C/T
391738	chr19	958669	109.01	G/A	G/A
391741	chr19	966155	299.77	T/C	T/C
391742	chr19	966255	155.01	T/A	T/A
391743	chr19	966258	144.01	A/G	A/G
391745	chr19	966445	332.01	T/C	T/C
391746	chr19	966448	394.01	A/G	A/G
391748	chr19	967021	391.01	A/G	A/G
391749	chr19	967053	562.01	T/A	T/A
391750	chr19	967060	501.01	T/C	T/C
391753	chr19	967584	101.51	C/C	C/C
391754	chr19	967917	250.01	T/C	T/C
391755	chr19	968031	470.01	T/C	T/C
391756	chr19	968150	391.06	A/G	G/G
391758	chr19	1025134	43.76	A/A	G/A
391759	chr19	1025136	43.76	A/A	T/A
391760	chr19	1059486	382	G/G	G/G
391762	chr19	1059555	37.01	C/T	C/T
391763	chr19	1061377	67.97	G/G	G/G
391764	chr19	1061380	67.97	A/A	A/A
391765	chr19	1061478	67.97	G/G	G/G
391766	chr19	1061485	67.97	G/G	G/G
391767	chr19	1076718	211.27	A/T	A/T
391768	chr19	1078173	127.07	T/C	C/C
391771	chr19	1100930	49.76	C/C	C/C
391772	chr19	1100976	47.76	C/C	C/C
391773	chr19	1120472	101.51	C/C	C/C
391774	chr19	1120480	101.51	C/C	C/C
391775	chr19	1120493	101.51	A/A	A/A
391776	chr19	1120495	101.51	T/T	T/T
391777	chr19	1120503	101.51	T/T	T/T
391778	chr19	1120514	101.51	A/A	A/A
391779	chr19	1120693	119.07	A/G	G/G
391780	chr19	1142761	2474	A/A	A/A
391781	chr19	1142786	35.77	T/T	C/T
391783	chr19	1176955	162.13	C/C	T/C
391784	chr19	1176963	134.26	C/C	T/C
391787	chr19	1178741	1381	T/T	T/T
391788	chr19	1178745	1461	C/C	C/C
391789	chr19	1178768	128.01	T/C	T/C
391790	chr19	1184956	678	G/G	G/G
391791	chr19	1184964	678	G/G	G/G
391792	chr19	1185312	86.01	T/A	T/A
391793	chr19	1185314	86.01	T/C	T/C
391794	chr19	1188756	80.01	T/C	T/C
391795	chr19	1188829	109.02	A/G	A/G
391797	chr19	1188908	431.01	A/T	A/T
391801	chr19	1189225	124.01	A/T	A/T
391802	chr19	1189232	161.01	G/A	G/A
391803	chr19	1189814	463	C/C	T/C
391807	chr19	1194065	134.26	T/T	C/T
391808	chr19	1194158	134.26	A/A	G/A
391809	chr19	1194167	134.26	C/C	T/C
391810	chr19	1201542	305.01	C/C	C/C
391812	chr19	1212756	58.02	T/G	T/G
391814	chr19	1212778	577.23	T/C	A/C
391815	chr19	1213018	703	C/C	C/C
391816	chr19	1306280	179.13	T/T	T/T
391817	chr19	1306579	31.02	T/C	T/C
391818	chr19	1306837	437	C/C	C/C
391819	chr19	1319693	41.76	T/T	T/T
391820	chr19	1319993	234.03	T/T	A/T
391822	chr19	1320656	155.01	A/T	A/T
391823	chr19	1320657	193.01	T/C	T/C
391826	chr19	1320991	112.04	A/G	G/G
391828	chr19	1329002	345.76	C/C	C/C
391833	chr19	1329919	1177	T/T	A/T
391835	chr19	1330168	744	C/C	C/C
391836	chr19	1330984	56.97	A/A	C/A
391837	chr19	1335177	977.01	A/T	A/T
391838	chr19	1335224	160.01	A/G	A/G
391839	chr19	1335295	958.01	A/T	A/T
391840	chr19	1335615	2234	C/C	C/C
391841	chr19	1335638	67.97	G/G	A/G
391845	chr19	1341831	301	G/G	G/G
391846	chr19	1341839	241.98	A/G	G/G
391847	chr19	1341932	116.01	T/A	T/A
391848	chr19	1341945	213.01	A/G	A/G
391852	chr19	1342450	84.01	T/A	T/A
391853	chr19	1342499	75.01	G/A	G/A
391855	chr19	1342747	1100	A/A	A/A
391856	chr19	1342750	1010.01	G/G	A/G
391858	chr19	1342760	147.01	C/T	C/T
391867	chr19	1346232	52.01	T/C	T/C
391869	chr19	1346238	323.01	G/T	G/T
391870	chr19	1346247	512.22	A/T	A/T
391871	chr19	1346352	606.01	A/G	A/G
391873	chr19	1346548	386.01	G/C	G/C
391874	chr19	1346574	148.01	A/G	A/G
391875	chr19	1346596	217.01	A/G	A/G
391876	chr19	1346607	110.01	T/G	T/G
391877	chr19	1346616	153.01	A/C	A/T
391880	chr19	1346878	567	C/C	C/C
391881	chr19	1346884	567	C/C	C/C
391882	chr19	1347518	207.13	C/C	C/C
391884	chr19	1485568	135.51	G/G	A/G
391885	chr19	1485671	43.01	T/C	C/C
391889	chr19	1545304	101.51	G/G	G/G
391890	chr19	1545413	101.51	A/A	A/A
391893	chr19	1562510	565.01	T/C	T/C
391894	chr19	1562520	596.01	C/T	C/T
391896	chr19	1562818	248.06	A/A	A/A
391900	chr19	1586910	61.01	T/C	C/C
391902	chr19	1586983	137.26	G/G	G/G
391903	chr19	1594228	109.51	C/C	C/C
391904	chr19	1594233	66.02	A/T	T/T
391905	chr19	1594859	108.51	C/C	C/C
391906	chr19	1601151	15

Hi yksrmc,

The perl script given before now does the job, only that you have to change just some stuff to adapt the script to what you needed.

However, I did modify the script to work with the new file attached to your last mail.
Please note you would have to change the condition as the case may be. I only added the new condition you gave. Please also see my output result attached to this mail as well.

Below is the script used:

#!/usr/bin/perl
use warnings;
use strict;
use Carp qw(croak);

croak "Usage: perl_script.pl <file_to_check.txt>"
  unless defined $ARGV[0];

my $filename = $ARGV[0];
my $counter  = {};

open my $fh, '<', $filename or croak "can't open $filename: $!";

while (<$fh>) {
    my ( $number1, $chr_name, $number2, $value, $gt_1, $gt_2 ) = split;

    $counter->{'A/T'}{'A/A'}++ if $gt_1 eq 'A/T' and $gt_2 eq 'A/A';
    $counter->{'G/C'}{'C/C'}++ if $gt_1 eq 'G/C' and $gt_2 eq 'C/C';
    $counter->{'A/G'}{'G/G'}++ if $gt_1 eq 'A/G' and $gt_2 eq 'G/G';

    print $_, $/ if $gt_1 ne $gt_2 and $gt_1 ne ( 'C/C' or 'A/A' );
}
close $fh or croak "can't close file: $!";

print map {
    sprintf "The Total Number of %s converted to %s is %d\n",
      $_, %{ $counter->{$_} }
} keys %$counter;

The conitions I used are as follows:
1. Print the present line from the file if and only if, the variable $gt_1 is not equal to $gt_2 AND the varibale $gt_1 is not equal to either 'C/C' or 'A/A',
2. count for the line if varibale $gt_1 is equal to 'A/G' and $gt_2 equal to 'G/G', the same logic is used for other count.

Hope this helps

Attachments
391440	chr19	261481	112.04	T/C	C/C

391446	chr19	297336	339	T/T	G/T

391456	chr19	298004	89.04	A/G	G/G

391457	chr19	298005	89.04	T/A	A/A

391458	chr19	298008	89.04	A/G	G/G

391462	chr19	317203	150.26	A/A	G/A

391512	chr19	521705	89.04	A/G	G/G

391513	chr19	521707	89.04	G/T	T/T

391516	chr19	522279	152.26	T/T	A/T

391525	chr19	552060	173.14	A/T	T/T

391537	chr19	553116	35.77	G/G	C/G

391539	chr19	553185	295	A/A	G/A

391547	chr19	560551	35.77	T/T	G/T

391560	chr19	562134	602.01	A/C	C/C

391569	chr19	636141	33.01	C/T	T/T

391599	chr19	684246	101.51	G/G	A/G

391600	chr19	684251	101.51	T/T	C/T

391619	chr19	701187	113.01	T/C	C/C

391628	chr19	712410	1131.01	A/G	G/G

391641	chr19	716207	34.12	T/A	A/A

391663	chr19	744880	323.46	C/T	G/C

391670	chr19	745675	375.76	A/A	G/A

391673	chr19	754610	253.01	C/G	G/G

391674	chr19	754621	455.01	T/C	C/C

391683	chr19	759615	103.01	C/T	T/T

391693	chr19	770092	395.01	A/G	G/G

391700	chr19	777295	213.06	G/G	A/G

391701	chr19	777306	213.06	A/A	T/A

391756	chr19	968150	391.06	A/G	G/G

391758	chr19	1025134	43.76	A/A	G/A

391759	chr19	1025136	43.76	A/A	T/A

391768	chr19	1078173	127.07	T/C	C/C

391779	chr19	1120693	119.07	A/G	G/G

391781	chr19	1142786	35.77	T/T	C/T

391807	chr19	1194065	134.26	T/T	C/T

391808	chr19	1194158	134.26	A/A	G/A

391814	chr19	1212778	577.23	T/C	A/C

391820	chr19	1319993	234.03	T/T	A/T

391826	chr19	1320991	112.04	A/G	G/G

391833	chr19	1329919	1177	T/T	A/T

391836	chr19	1330984	56.97	A/A	C/A

391841	chr19	1335638	67.97	G/G	A/G

391846	chr19	1341839	241.98	A/G	G/G

391856	chr19	1342750	1010.01	G/G	A/G

391877	chr19	1346616	153.01	A/C	A/T

391884	chr19	1485568	135.51	G/G	A/G

391885	chr19	1485671	43.01	T/C	C/C

391900	chr19	1586910	61.01	T/C	C/C

391904	chr19	1594233	66.02	A/T	T/T

391906	chr19	1601151	156.07	A/G	G/G

391930	chr19	1681805	165.14	T/C	C/C

391940	chr19	1702719	37.02	T/T	G/G

391946	chr19	1710873	383.33	A/A	T/A

391961	chr19	1798731	71.01	T/C	C/C

391979	chr19	1804412	36.79	G/G	T/G

391981	chr19	1804424	67.97	T/T	C/T

391994	chr19	1891315	385.01	T/C	C/C

391995	chr19	1891317	385.01	T/C	C/C

392008	chr19	1892828	118.01	A/C	C/C

392009	chr19	1892831	138.01	A/T	T/T

392023	chr19	1894783	249.98	T/A	A/A

392033	chr19	1900062	165.04	C/A	A/A

392037	chr19	1939044	179.13	A/A	T/A

392055	chr19	1994545	60.01	A/G	G/G

392085	chr19	2072424	104.01	T/A	A/A

392086	chr19	2072426	104.01	G/C	C/C

392120	chr19	2143094	50.76	G/G	A/G

392129	chr19	2152678	48.01	T/C	C/C

392135	chr19	2155355	109.51	G/G	A/G

392164	chr19	2218627	109.01	A/C	C/C

392166	chr19	2218893	153.03	T/C	C/C

392170	chr19	2277788	189.77	A/T	T/T

392205	chr19	2387288	112.04	T/A	A/A

392214	chr19	2400535	388	G/G	A/G

392222	chr19	2401055	360.01	A/G	G/G

392236	chr19	2405916	835.46	A/G	G/G

392252	chr19	2417259	160.13	A/A	T/A

392266	chr19	2471167	34.12	G/T	T/T

392283	chr19	2505515	43.76	T/T	C/T

392284	chr19	2507878	293.18	C/G	G/G

392288	chr19	2508402	345.01	T/C	C/C

392289	chr19	2508405	338.01	A/G	G/G

392303	chr19	2517199	36.02	A/G	G/G

392304	chr19	2517201	36.02	G/A	A/A

392305	chr19	2517583	158.26	G/G	A/G

392312	chr19	2520166	248.06	G/G	A/G

392321	chr19	2531961	67.97	A/A	G/A

392347	chr19	2572492	89.04	T/C	C/C

392349	chr19	2596491	417.01	C/T	T/T

392361	chr19	2598401	58.76	A/A	C/A

392365	chr19	2603280	36.02	A/G	G/G

392366	chr19	2603872	119.04	A/G	G/G

392367	chr19	2612912	278.18	A/T	T/T

392399	chr19	2667711	98.01	A/G	G/G

392403	chr19	2681212	66.02	T/C	C/C

392404	chr19	2681399	227.27	C/T	T/T

392405	chr19	2681400	227.27	T/C	C/C

392422	chr19	2725372	83.01	T/A	A/A

392423	chr19	2725374	86.01	T/C	C/C

392424	chr19	2729621	107.07	A/G	G/G

392425	chr19	2729627	119.79	A/G	G/G

392444	chr19	2821688	47.02	T/C	C/C

392445	chr19	2821691	47.02	G/A	A/A

392446	chr19	2821698	47.02	G/C	C/C

392447	chr19	2826120	196.01	A/T	T/T

392448	chr19	2826125	261.77	C/T	T/T

392449	chr19	2826126	261.77	A/G	G/G

392477	chr19	2831947	242.03	G/G	T/G

392486	chr19	2868637	815	T/T	A/T

392516	chr19	2874188	318.98	G/C	C/C

392537	chr19	2890388	150.07	T/C	C/C

392542	chr19	2908625	284.01	T/T	C/T

392547	chr19	2928211	234.03	G/G	A/G

392548	chr19	2928219	234.03	G/G	A/G

392553	chr19	2929153	697.54	G/G	A/G

392573	chr19	2932576	124.51	A/A	T/A

392585	chr19	2954615	1834	A/A	G/A

392587	chr19	2954739	304.77	A/G	G/G

392598	chr19	2959419	262.03	G/G	A/G

392609	chr19	2966188	913	G/G	A/G

392610	chr19	2966202	929	G/G	A/G

392626	chr19	2969717	423.06	C/G	G/G

392647	chr19	2971025	1944.01	T/A	A/A

392664	chr19	2988577	272.09	C/G	G/G

392665	chr19	2988581	332.34	A/G	G/G

392682	chr19	2999826	175.13	A/A	T/A

392714	chr19	3082977	72.87	G/T	G/A

392723	chr19	3086273	428.01	T/C	C/C

392724	chr19	3086486	366.77	G/G	A/G

392728	chr19	3086800	544.09	T/G	G/G

392736	chr19	3157017	7405.01	T/C	C/C

392744	chr19	3158376	5470.01	A/T	T/T

392796	chr19	3214848	414.01	A/T	T/T

392803	chr19	3215795	170.01	G/C	C/C

392805	chr19	3218344	193.03	C/G	G/G

392806	chr19	3218349	189.04	G/A	A/A

392845	chr19	3288310	468	A/A	G/A

392846	chr19	3288315	435	A/A	T/A

392850	chr19	3331038	60.02	T/A	A/A

392851	chr19	3331040	34.02	T/C	C/C

392869	chr19	3396741	242.52	A/G	G/G

392873	chr19	3399856	696.64	A/G	G/G

392887	chr19	3400644	35.77	T/T	G/T

392907	chr19	3408822	101.01	A/T	T/T

392908	chr19	3408833	173.14	T/C	C/C

392914	chr19	3410021	135.26	T/T	C/T

392917	chr19	3411548	79.97	T/T	A/T

392946	chr19	3424246	298.64	C/G	G/G

392962	chr19	3436048	116.01	A/T	T/T

392963	chr19	3436053	210.52	C/T	T/T

392967	chr19	3436329	342.01	A/A	T/A

392968	chr19	3436496	474.02	T/C	C/C

392969	chr19	3436504	470.01	T/C	C/C

392984	chr19	3451910	116.51	A/A	T/A

392985	chr19	3451913	116.51	G/G	A/G

393004	chr19	3560899	75.97	G/G	C/G

393005	chr19	3560902	75.97	A/A	T/A

393011	chr19	3565223	234.03	G/G	C/G

393014	chr19	3565561	327.01	A/T	T/T

393015	chr19	3565562	329.01	G/C	C/C

393017	chr19	3581346	264.98	A/T	T/T

393023	chr19	3581632	280.98	A/G	G/G

393041	chr19	3598554	156.13	T/T	A/T

393054	chr19	3602505	46.01	A/T	A/C

393137	chr19	3727692	257.52	T/C	C/C

393152	chr19	3742201	35.77	G/G	A/G

393158	chr19	3744427	35.77	G/G	T/G

393160	chr19	3758275	36.01	A/G	G/G

393186	chr19	3874477	35.77	G/G	A/G

393197	chr19	3896097	44.01	T/G	T/A

393237	chr19	3919071	95.01	T/A	A/A

393238	chr19	3919255	86.01	T/C	C/C

393239	chr19	3919264	121.01	A/G	G/G

393258	chr19	3927014	767.01	T/A	A/A

393262	chr19	3929034	91.97	G/G	A/G

393266	chr19	3930236	566.01	G/C	C/C

393287	chr19	3987315	688.01	A/G	G/G

393289	chr19	3988850	116.02	A/C	C/C

393290	chr19	3989161	829.01	A/G	G/G

393297	chr19	3989626	2009.01	T/A	A/A

393303	chr19	3989894	47.03	A/G	G/G

393325	chr19	3997178	479.45	T/T	A/T

393326	chr19	3997566	311.01	T/C	C/C

393327	chr19	3997575	377.02	C/G	G/G

393329	chr19	4021364	412.01	T/C	C/C

393330	chr19	4021367	417.02	A/T	T/T

393360	chr19	4071079	142.26	A/A	G/A

393369	chr19	4079762	903.54	A/A	G/A

393372	chr19	4079922	58.02	A/T	T/T

393401	chr19	4135856	127.07	A/T	T/T

393402	chr19	4135974	121.01	T/C	C/C

393404	chr19	4136674	141.14	A/G	G/G

393405	chr19	4136676	111.01	A/T	T/T

393416	chr19	4146267	32.77	T/T	A/T

393420	chr19	4147641	134.26	A/A	G/A

393422	chr19	4148618	49.01	G/A	A/A

393423	chr19	4148628	116.01	G/C	C/C

393441	chr19	4156524	199.52	T/C	C/C

393445	chr19	4163724	75.97	G/G	A/G

393448	chr19	4168218	241.64	A/T	T/T

393450	chr19	4203982	101.51	A/A	G/A

393452	chr19	4209665	329	G/G	C/G

393453	chr19	4209672	462	T/T	A/T

393470	chr19	4223919	58.01	A/T	T/T

393473	chr19	4225467	355	T/T	A/T

393489	chr19	4227498	242.09	T/C	C/C

393490	chr19	4227507	242.18	A/G	G/G

393491	chr19	4231755	756.04	A/G	G/G

393501	chr19	4231950	398.1	A/A	G/A

393502	chr19	4231952	398.1	A/A	G/A

393505	chr19	4231976	431.05	T/T	C/T

393506	chr19	4231989	442.64	T/T	C/T

393508	chr19	4231998	417.45	A/A	C/A

393509	chr19	4232006	441.79	G/G	A/G

393533	chr19	4239928	365.97	A/A	T/A

393544	chr19	4242662	211.27	T/C	C/C

393545	chr19	4242665	211.27	A/T	T/T

393548	chr19	4243509	30.01	C/T	T/T

393552	chr19	4245397	153.26	G/G	A/G

393557	chr19	4254848	67.97	A/A	T/A

393575	chr19	4287198	44.76	A/A	G/A

393579	chr19	4287577	284.19	A/A	T/A

393582	chr19	4289591	43.76	G/G	A/G

393584	chr19	4291878	70.02	G/T	T/T

393586	chr19	4292370	43.02	A/G	G/G

393587	chr19	4293312	185.01	C/T	T/T

393591	chr19	4293781	406.03	T/C	C/C

393596	chr19	4302658	66.01	T/A	A/A

393599	chr19	4308853	507	T/T	G/T

393600	chr19	4309043	540.07	G/A	A/A

393606	chr19	4310020	2101.09	T/A	A/A

393639	chr19	4345068	134.26	G/G	A/G

393708	chr19	4416682	442.01	T/A	A/A

393725	chr19	4425473	249.03	T/T	A/T

393763	chr19	4469320	94.01	G/T	T/T

393792	chr19	4484007	322.2	T/C	C/C

393793	chr19	4484029	360.21	A/A	G/A

393794	chr19	4484078	491	G/G	A/G

393797	chr19	4484377	974.01	G/A	A/A

393812	chr19	4509469	1436.01	A/C	C/C

393818	chr19	4510168	1293.79	A/G	G/G

393861	chr19	4561978	155.14	T/C	C/C

393921	chr19	4609622	376	G/G	A/G

393923	chr19	4609814	111.04	T/G	G/G

393937	chr19	4619798	415.2	G/A	A/A

393983	chr19	4626590	63.77	A/A	T/A

393989	chr19	4643086	50.76	A/A	T/A

393994	chr19	4646877	885.06	C/G	A/C

394000	chr19	4667375	121.02	T/C	A/C

394005	chr19	4686019	272.77	G/A	A/A

394015	chr19	4697106	632.01	A/G	G/G

394030	chr19	4726609	693	G/G	C/G

394054	chr19	4753336	35.77	G/G	A/G

394055	chr19	4753437	35.77	A/A	T/A

394057	chr19	4756518	66.03	T/A	A/A

394058	chr19	4756520	66.09	T/C	C/C

394067	chr19	4774900	2506	A/A	C/A

394080	chr19	4787754	150.14	A/G	G/G

394114	chr19	4841912	510	G/G	A/G

394124	chr19	4843515	501.03	A/G	G/G

394144	chr19	4846508	1812.01	T/C	C/C

394154	chr19	4850156	49.01	T/C	C/C

394155	chr19	4850157	46.01	T/C	C/C

394182	chr19	4863626	161.14	G/A	A/A

394183	chr19	4863628	172.14	G/C	C/C

394192	chr19	4871509	289.01	G/G	A/G

394194	chr19	4871516	342	T/T	A/T

394234	chr19	4883541	50.76	T/T	A/T

394236	chr19	4884163	66.01	A/T	T/T

394242	chr19	4896117	47.02	G/A	A/A

394243	chr19	4896122	47.02	T/A	A/A

394244	chr19	4896124	47.02	T/C	C/C

394273	chr19	4940907	109.01	A/T	T/T

394274	chr19	4940937	200.14	A/A	G/A

394286	chr19	4974096	544.01	G/A	A/A

394287	chr19	4974099	578.01	A/G	G/G

394334	chr19	5169211	204.01	A/G	G/G

394340	chr19	5172508	44.01	T/C	C/C

394351	chr19	5175887	142.26	G/G	A/G

394373	chr19	5270876	603.22	A/G	G/G

394374	chr19	5270878	591.01	A/T	T/T

394381

Yes, Finally I got the output which I was really looking for..Thanks 2teez for ypur time..:)

Edited 1 Year Ago by Dani: Formatting fixed

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