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maf2maf/maf2vcf: Better tests, and multiallelic handling
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@ckandoth
ckandoth committed Feb 24, 2018
1 parent 7af04c0 commit 1ce59ed
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9 changes: 5 additions & 4 deletions maf2maf.pl
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Expand Up @@ -17,7 +17,7 @@
my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count );
my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4, 5000, 0 );
my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz", "$ENV{HOME}/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz" );
my ( $species, $ncbi_build, $cache_version, $maf_center, $min_hom_vaf, $max_filter_ac ) = ( "homo_sapiens", "GRCh37", "", ".", 0.7, 10 );
my ( $species, $ncbi_build, $cache_version, $maf_center, $max_filter_ac ) = ( "homo_sapiens", "GRCh37", "", ".", 10 );
my $perl_bin = $Config{perlpath};

# Columns that can be safely borrowed from the input MAF
Expand Down Expand Up @@ -267,7 +267,8 @@
else {
# Extract minimal variant info, and figure out which of the tumor alleles is non-REF
my ( $chr, $pos, $ref, $al1, $al2, $sample_id ) = map{ my $c = lc; ( defined $input_maf_col_idx{$c} ? $cols[$input_maf_col_idx{$c}] : "" ) } qw( Chromosome Start_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode );
my $var = (( defined $al1 and $al1 and $al1 ne $ref ) ? $al1 : $al2 );
# Prefer Tumor_Seq_Allele2 over Tumor_Seq_Allele1 if both are non-REF
my $var = (( defined $al2 and $al2 and $al2 ne $ref ) ? $al2 : $al1 );

# Remove any prefixed reference bps from alleles, using "-" for simple indels
while( $ref and $var and substr( $ref, 0, 1 ) eq substr( $var, 0, 1 ) and $ref ne $var ) {
Expand All @@ -277,10 +278,10 @@

# Create a key for this variant using Chromosome:Start_Position:Tumor_Sample_Barcode:Reference_Allele:Variant_Allele
my $key = join( ":", $chr, $pos, $sample_id, $ref, $var );
%{$input_maf_data{$key}} = ();

# Store values for this variant into a hash, adding column names to the key
foreach my $c ( map{lc} split( ",", $retain_cols )) {
$input_maf_data{$key}{$c} = "";
if( defined $input_maf_col_idx{$c} and defined $cols[$input_maf_col_idx{$c}] ) {
$input_maf_data{$key}{$c} = $cols[$input_maf_col_idx{$c}];
}
Expand Down Expand Up @@ -319,7 +320,7 @@
my $key = join( ":", map{ my $c = lc; $cols[$output_maf_col_idx{$c}] } qw( Chromosome Start_Position Tumor_Sample_Barcode Reference_Allele Tumor_Seq_Allele2 ));
foreach my $c ( map{lc} split( /\t/, $maf_header )){
if( !$force_new_cols{$c} ) {
$cols[$output_maf_col_idx{$c}] = ( defined $input_maf_data{$key}{$c} ? $input_maf_data{$key}{$c} : "" );
$cols[$output_maf_col_idx{$c}] = $input_maf_data{$key}{$c} if( defined $input_maf_data{$key}{$c} );
}
}
$tmp_tn_maf_fh->print( join( "\t", @cols ) . "\n" );
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9 changes: 7 additions & 2 deletions maf2vcf.pl
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Expand Up @@ -201,8 +201,13 @@
$al1 = $ref if( $al1 eq "" );
$al2 = $ref if( $al2 eq "" );

# Handle a case when $al1 is a SNP we want to annotate, but $al2 is incorrectly "-"
( $al1, $al2 ) = ( $al2, $al1 ) if( $al2 eq "-" );
# When variant alleles are a SNP and a "-", warn user of misusing "-" to denote REF
if( $al1 ne $ref and $al2 ne $ref and $al1 ne $al2 and ( $al1 eq "-" or $al2 eq "-" ) and
length( $al1 ) == 1 and length( $al2 ) == 1 and length( $ref ) == 1 ) {
$al1 = $ref if( $al1 eq "-" );
$al2 = $ref if( $al2 eq "-" );
warn "WARNING: Replacing '-' with reference allele in: $line";
}

# Blank out the dashes (or other weird chars) used with indels
( $ref, $al1, $al2, $n_al1, $n_al2 ) = map{s/^(\?|-|0)+$//; $_} ( $ref, $al1, $al2, $n_al1, $n_al2 );
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18 changes: 16 additions & 2 deletions tests/maf2maf.t
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Expand Up @@ -11,7 +11,21 @@ my $script_dir = dirname( $test_dir );
chdir $script_dir;

# Set the number of tests we'll run, and run them
use Test::Simple tests => 3;
use Test::Simple tests => 8;
ok( system( "perl maf2maf.pl --help > /dev/null" ) == 0 );
ok( system( "perl maf2maf.pl --man > /dev/null" ) == 0 );
ok( system( "perl maf2maf.pl --input-maf tests/test.maf --output-maf tests/test.vep.maf --custom-enst data/isoform_overrides_at_mskcc" ) == 0 );

# Test standard operation, diff, and cleanup
ok( system( "perl maf2maf.pl --input-maf tests/test.maf --output-maf tests/test_output.vep_isoforms.new.maf" ) == 0 );
ok( system( "bash -c 'diff <(cut -f58,95 --complement tests/test_output.vep_isoforms.maf) <(cut -f58,95 --complement tests/test_output.vep_isoforms.new.maf)'" ) == 0 );
system( "rm -f tests/test_output.vep_isoforms.new.maf" );

# Test standard operation with the TSV file with minimal MAF columns, diff, and cleanup
ok( system( "perl maf2maf.pl --input-maf tests/test.tsv --output-maf tests/test_output.vep_isoforms.new.maf" ) == 0 );
ok( system( "bash -c 'diff <(cut -f58,95 --complement tests/test_output.vep_isoforms.maf) <(cut -f58,95 --complement tests/test_output.vep_isoforms.new.maf)'" ) == 0 );
system( "rm -f tests/test_output.vep_isoforms.new.maf" );

# Test using Uniprot's canonical isoforms as overrides, diff, and cleanup
ok( system( "perl maf2maf.pl --input-maf tests/test.maf --output-maf tests/test_output.custom_isoforms.new.maf --custom-enst data/isoform_overrides_uniprot" ) == 0 );
ok( system( "bash -c 'diff <(cut -f58,95 --complement tests/test_output.custom_isoforms.maf) <(cut -f58,95 --complement tests/test_output.custom_isoforms.new.maf)'" ) == 0 );
system( "rm -f tests/test_output.custom_isoforms.new.maf" );
13 changes: 11 additions & 2 deletions tests/maf2vcf.t
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Expand Up @@ -11,7 +11,16 @@ my $script_dir = dirname( $test_dir );
chdir $script_dir;

# Set the number of tests we'll run, and run them
use Test::Simple tests => 3;
use Test::Simple tests => 6;
ok( system( "perl maf2vcf.pl --help > /dev/null" ) == 0 );
ok( system( "perl maf2vcf.pl --man > /dev/null" ) == 0 );
ok( system( "perl maf2vcf.pl --input-maf tests/test.maf --output-dir tests/vcfs --per-tn-vcfs" ) == 0 );

# Test standard operation, diff, and cleanup
ok( system( "perl maf2vcf.pl --input-maf tests/test.maf --output-dir tests --output-vcf tests/test_vcf2vcf.new.vcf" ) == 0 );
ok( system( "diff tests/test_vcf2vcf.vcf tests/test_vcf2vcf.new.vcf" ) == 0 );
system( "rm -f tests/test_vcf2vcf.new.vcf tests/test.pairs.tsv" );

# Test standard operation with the TSV file with minimal MAF columns, diff, and cleanup
ok( system( "perl maf2vcf.pl --input-maf tests/test.tsv --output-dir tests --output-vcf tests/test_vcf2vcf.new.vcf" ) == 0 );
ok( system( "diff tests/test_vcf2vcf.vcf tests/test_vcf2vcf.new.vcf" ) == 0 );
system( "rm -f tests/test_vcf2vcf.new.vcf tests/test.pairs.tsv" );
40 changes: 20 additions & 20 deletions tests/test.maf
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@@ -1,22 +1,22 @@
#version 2.4
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count
MTOR 2475 . GRCh37 1 11290179 11290179 + Intron DEL A A - rs35067541 TUMOR NORMAL A A 20 10 10 35 30 5
Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA novel TUMOR NORMAL TG TG 16 11 5 22 21 1
CHD1L 9557 . GRCh37 1 146728217 146728217 + Splice_Site SNP G G A novel TUMOR NORMAL G G 40 19 21 42 42 0
INHA 3623 . GRCh37 2 220439700 220439701 + Frame_Shift_Ins INS - - CT novel TUMOR NORMAL - - 93 21 72 51 51 0
BAP1 8314 . GRCh37 3 52437427 52437448 + Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - novel TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 20 10 10 11 11 0
BAP1 8314 . GRCh37 3 52437702 52437708 + Frame_Shift_Del DEL TGGGTGA TGGGTGA - novel TUMOR NORMAL TGGGTGA TGGGTGA 20 10 10 11 11 0
BAP1 8314 . GRCh37 3 52443789 52443850 + Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - novel TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 20 10 10 11 11 0
PIK3CA 5290 . GRCh37 3 178928219 178928220 + In_Frame_Ins INS - - ATA TUMOR NORMAL - - 43 21 22 11 11 0
TERT 7015 . GRCh37 5 1295228 1295228 + 5'Flank SNP G G A novel TUMOR NORMAL G G 20 10 10 11 11 0
TERT 7015 . GRCh37 5 1295250 1295250 + 5'Flank SNP G G A novel TUMOR NORMAL G G 20 10 10 11 11 0
MAP3K1 4214 . GRCh37 5 56177849 56177851 + In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA 50 34 16 46 46 0
APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - novel TUMOR NORMAL AAGA AAGA 20 12 8 32 30 2
APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA novel TUMOR NORMAL AAGA AAGA 20 12 8 32 30 2
APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA GA - novel TUMOR NORMAL - - 20 0 8 32 0 2
APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - novel TUMOR NORMAL AAGA GA 20 12 8 32 30 0
APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA novel TUMOR NORMAL AAGA - 20 12 8 32 30 0
CCND3 896 . GRCh37 6 41903782 41903783 + Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG 50 28 22 48 48 0
MET 4233 . GRCh37 7 116412043 116412043 + Missense_Mutation SNP G G C novel TUMOR NORMAL G G 47 25 22 99 98 1
FLT3 2322 . GRCh37 13 28608242 28608243 + In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG novel TUMOR NORMAL - - 20 10 10 11 11 0
TP53 7157 . GRCh37 17 7579312 7579312 + Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C 42 20 22 19 18 1
MTOR 0 . GRCh37 1 11290179 11290179 + Intron DEL A A - TUMOR NORMAL A A 20 10 10 35 30 5
Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA TUMOR NORMAL TG TG 16 11 5 22 21 1
CHD1L 0 . GRCh37 1 146728217 146728217 + Splice_Site SNP G G A TUMOR NORMAL G G 40 19 21 42 42 0
INHA 0 . GRCh37 2 220439700 220439701 + Frame_Shift_Ins INS - - CT TUMOR NORMAL - - 93 21 72 51 51 0
BAP1 0 . GRCh37 3 52437427 52437448 + Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 20 10 10 11 11 0
BAP1 0 . GRCh37 3 52437702 52437708 + Frame_Shift_Del DEL TGGGTGA TGGGTGA - TUMOR NORMAL TGGGTGA TGGGTGA 20 10 10 11 11 0
BAP1 0 . GRCh37 3 52443789 52443850 + Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 20 10 10 11 11 0
PIK3CA 0 . GRCh37 3 178928219 178928220 + In_Frame_Ins INS - - ATA TUMOR NORMAL - - 43 21 22 11 11 0
PIK3CA 0 . GRCh37 3 178936091 178936091 + Missense_Mutation SNP G - A TUMOR NORMAL G G 43 21 22 11 11 0
TERT 0 . GRCh37 5 1295228 1295228 + 5'Flank SNP G G A TUMOR NORMAL G G 20 10 10 11 11 0
TERT 0 . GRCh37 5 1295250 1295250 + 5'Flank SNP G G A TUMOR NORMAL G G 20 10 10 11 11 0
MAP3K1 0 . GRCh37 5 56177849 56177851 + In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA 50 34 16 46 46 0
APC 0 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA TUMOR NORMAL AAGA AAGA 20 12 8 32 30 2
APC 0 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA - CA TUMOR NORMAL - - 20 0 8 32 0 2
APC 0 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - TUMOR NORMAL AAGA GA 20 12 8 32 30 0
APC 0 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA TUMOR NORMAL AAGA - 20 12 8 32 30 0
CCND3 0 . GRCh37 6 41903782 41903783 + Missense_Mutation DNP AG AG CA TUMOR NORMAL AG AG 50 28 22 48 48 0
MET 0 . GRCh37 7 116412043 116412043 + Missense_Mutation SNP G G C TUMOR NORMAL G G 47 25 22 99 98 1
FLT3 0 . GRCh37 13 28608242 28608243 + In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR NORMAL - - 20 10 10 11 11 0
TP53 0 . GRCh37 17 7579312 7579312 + Splice_Region SNP C C A TUMOR NORMAL C C 42 20 22 19 18 1
42 changes: 21 additions & 21 deletions tests/test.tsv
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@@ -1,21 +1,21 @@
Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Tumor_Sample_Barcode t_depth t_ref_count t_alt_count
1 11290179 A - TUMOR 20 10 10
1 15557977 TG CA TUMOR 16 11 5
1 146728217 G A TUMOR 40 19 21
2 220439700 - CT TUMOR 93 21 72
3 52437427 CCCACCTGTCAGCGCCAGGGGA - TUMOR 20 10 10
3 52437702 TGGGTGA - TUMOR 20 10 10
3 52443789 TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR 20 10 10
3 178928219 - ATA TUMOR 43 21 22
5 1295228 G A TUMOR 20 10 10
5 1295250 G A TUMOR 20 10 10
5 56177849 CAA - TUMOR 50 34 16
5 112174758 AAGA - TUMOR 20 12 8
5 112174758 AAGA GA TUMOR 20 12 8
5 112174758 AAGA - TUMOR 20 0 8
5 112174758 AAGA - TUMOR 20 12 8
5 112174758 AAGA GA TUMOR 20 12 8
6 41903782 AG CA TUMOR 50 28 22
7 116412043 G C TUMOR 47 25 22
13 28608242 - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR 20 10 10
17 7579312 C A TUMOR 42 20 22
Chromosome Start_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count
1 11290179 A A - TUMOR NORMAL A A 20 10 10 35 30 5
1 15557977 TG TG CA TUMOR NORMAL TG TG 16 11 5 22 21 1
1 146728217 G G A TUMOR NORMAL G G 40 19 21 42 42 0
2 220439700 - - CT TUMOR NORMAL - - 93 21 72 51 51 0
3 52437427 CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 20 10 10 11 11 0
3 52437702 TGGGTGA TGGGTGA - TUMOR NORMAL TGGGTGA TGGGTGA 20 10 10 11 11 0
3 52443789 TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 20 10 10 11 11 0
3 178928219 - - ATA TUMOR NORMAL - - 43 21 22 11 11 0
3 178936091 G - A TUMOR NORMAL G G 43 21 22 11 11 0
5 1295228 G G A TUMOR NORMAL G G 20 10 10 11 11 0
5 1295250 G G A TUMOR NORMAL G G 20 10 10 11 11 0
5 56177849 CAA CAA - TUMOR NORMAL CAA CAA 50 34 16 46 46 0
5 112174758 AAGA AAGA GA TUMOR NORMAL AAGA AAGA 20 12 8 32 30 2
5 112174758 AAGA - CA TUMOR NORMAL - - 20 0 8 32 0 2
5 112174758 AAGA AAGA - TUMOR NORMAL AAGA GA 20 12 8 32 30 0
5 112174758 AAGA AAGA GA TUMOR NORMAL AAGA - 20 12 8 32 30 0
6 41903782 AG AG CA TUMOR NORMAL AG AG 50 28 22 48 48 0
7 116412043 G G C TUMOR NORMAL G G 47 25 22 99 98 1
13 28608242 - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR NORMAL - - 20 10 10 11 11 0
17 7579312 C C A TUMOR NORMAL C C 42 20 22 19 18 1
25 changes: 25 additions & 0 deletions tests/test_vcf2vcf.vcf
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##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=G,Type=Integer,Description="Allelic Depths of REF and ALT(s) in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL
1 11290178 . TA T . . . GT:AD:DP 0/1:10,10:20 0/0:30,5:35
1 15557977 . TG CA . . . GT:AD:DP 0/1:11,5:16 0/0:21,1:22
1 146728217 . G A . . . GT:AD:DP 0/1:19,21:40 0/0:42,0:42
2 220439700 . G GCT . . . GT:AD:DP 0/1:21,72:93 0/0:51,0:51
3 52437426 . GCCCACCTGTCAGCGCCAGGGGA G . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11
3 52437701 . GTGGGTGA G . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11
3 52443788 . ATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC A . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11
3 178928219 . G GATA . . . GT:AD:DP 0/1:21,22:43 0/0:11,0:11
3 178936091 . G A . . . GT:AD:DP 0/1:21,22:43 0/0:11,0:11
5 1295228 . G A . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11
5 1295250 . G A . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11
5 56177848 . TCAA T . . . GT:AD:DP 0/1:34,16:50 0/0:46,0:46
5 112174757 . GAAGA GGA . . . GT:AD:DP 0/1:12,8:20 0/0:30,2:32
5 112174757 . GAAGA GCA,G . . . GT:AD:DP 1/2:0,8,.:20 2/2:0,2,.:32
5 112174757 . GAAGA G,GGA . . . GT:AD:DP 0/1:12,8,.:20 0/2:30,0,.:32
5 112174757 . GAAGA GGA,G . . . GT:AD:DP 0/1:12,8,.:20 0/2:30,0,.:32
6 41903782 . AG CA . . . GT:AD:DP 0/1:28,22:50 0/0:48,0:48
7 116412043 . G C . . . GT:AD:DP 0/1:25,22:47 0/0:98,1:99
13 28608242 . A AACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11
17 7579312 . C A . . . GT:AD:DP 0/1:20,22:42 0/0:18,1:19

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