diff --git a/test/aa.out b/test/aa.out index c08f4c109..3b2d46de4 100644 --- a/test/aa.out +++ b/test/aa.out @@ -1,5 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER= +##reference=file://some/path/human_g1k_v37.fasta ##contig= ##contig= ##contig= diff --git a/test/aa.vcf b/test/aa.vcf index 7bee378d4..14b953bd8 100644 --- a/test/aa.vcf +++ b/test/aa.vcf @@ -1,5 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER= +##reference=file://some/path/human_g1k_v37.fasta ##contig= ##contig= ##contig= diff --git a/test/ad-bias.vcf b/test/ad-bias.vcf index e14231b42..61e4f918b 100644 --- a/test/ad-bias.vcf +++ b/test/ad-bias.vcf @@ -1,5 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER= +##reference=file://some/path/human_g1k_v37.fasta ##contig= ##FORMAT= ##FORMAT= diff --git a/test/annotate.out b/test/annotate.out index 582318e4f..b0e0aba61 100644 --- a/test/annotate.out +++ b/test/annotate.out @@ -39,5 +39,5 @@ 2 3199812 indel_3199812 G GTT,GT 82.7 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:322:26 1/2:322:26 3 3212016 indel_3212016 CTT C,CT 79 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:91:26 1/2:91:26 4 3258448 indel_3258448 TACACACAC T 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31 -4 4000000 id1 T A,C 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31 +4 4000000 id1 T A,C 59.9 PASS AN=4;AC=2,0;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31 4 4000001 id2 T A 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31 diff --git a/test/annotate.vcf b/test/annotate.vcf index e85bc1117..87d8a81ef 100644 --- a/test/annotate.vcf +++ b/test/annotate.vcf @@ -35,5 +35,5 @@ 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26 4 3258448 . TACACACAC T 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 -4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 diff --git a/test/annotate2.out b/test/annotate2.out index 42b819ca5..284f8466a 100644 --- a/test/annotate2.out +++ b/test/annotate2.out @@ -39,5 +39,5 @@ 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26 4 3258448 . TACACACAC T 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 -4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 diff --git a/test/annotate3.out b/test/annotate3.out index b79930424..00de8de7b 100644 --- a/test/annotate3.out +++ b/test/annotate3.out @@ -36,5 +36,5 @@ 2 3199812 id11 G GTT,GT 99 PASS AN=4;AC=2,2;STR=id11 GT:GQ:DP 1/2:322:26 1/2:322:26 3 3212016 id12 CTT C,CT 99 PASS AN=4;AC=2,2;STR=id12 GT:GQ:DP 1/2:91:26 1/2:91:26 4 3258448 id13 TACACACAC T 99 PASS AN=4;AC=2;STR=id13 GT:GQ:DP 0/1:325:31 0/1:325:31 -4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 diff --git a/test/annots.vcf b/test/annots.vcf index cf2ae71b8..5ebcc6db4 100644 --- a/test/annots.vcf +++ b/test/annots.vcf @@ -27,7 +27,7 @@ 1 3062915 idSNP G T,C 99 PASS STR=testSNP;TEST=5;DP4=1,2,3,4;AN=3;AC=0,0 GT:TT:GQ:DP:GL 0|0:9,9:999:99:-99,-9,-99,-99,-9,-99 0:9,9:999:99:-99,-9,-99 1 3106154 id4 CAAA C 99 PASS STR=id4;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 1 3106154 id5 C CT 99 PASS STR=id5;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 -1 3157410 id6 GA GC,G 99 PASS STR=id6;AN=4;AC=0 GT:GQ:DP 0|0:99:99 0|0:99:99 +1 3157410 id6 GA GC,G 99 PASS STR=id6;AN=4;AC=0,0 GT:GQ:DP 0|0:99:99 0|0:99:99 1 3162006 id7 GAA GG 99 PASS STR=id7;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 1 3177144 id8 G T 99 PASS STR=id8;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 1 3177144 id9 G . 99 PASS STR=id9;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 diff --git a/test/check.vcf b/test/check.vcf index 055fd4342..79de593cc 100644 --- a/test/check.vcf +++ b/test/check.vcf @@ -12,6 +12,7 @@ ##contig= ##contig= ##contig= +##contig= ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta ##readme=AAAAAA ##readme=BBBBBB @@ -29,8 +30,8 @@ 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26 4 3258448 . TACACACAC T 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 -4 3258449 . GCAAA GA,G 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 -4 3258450 . AAAAGAAAAAG A,AAAAAAG 59.9 PASS DP=60;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258449 . GCAAA GA,G 59.9 PASS DP=62;AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31 +4 3258450 . AAAAGAAAAAG A,AAAAAAG 59.9 PASS DP=60;AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31 4 3258451 . AAA AGT 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 4 3258452 . AAA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 4 3258453 . AACA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 diff --git a/test/consensus.vcf b/test/consensus.vcf index 007aabfbf..54ca6ebee 100644 --- a/test/consensus.vcf +++ b/test/consensus.vcf @@ -1,7 +1,10 @@ ##fileformat=VCFv4.2 ##FORMAT= +##reference=file://some/path/human_g1k_v37.fasta ##INFO= ##ALT= +##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA001 1 5 . C a . PASS . GT 0/1 1 5 . C t . PASS . GT 0/1 diff --git a/test/consensus2.vcf b/test/consensus2.vcf index ca4c0595d..babbedcb3 100644 --- a/test/consensus2.vcf +++ b/test/consensus2.vcf @@ -2,6 +2,11 @@ ##FORMAT= ##INFO= ##ALT= +##reference=file://some/path/human_g1k_v37.fasta +##contig= +##contig= +##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA001 1 59 . C a,Caa . PASS . GT 1|2 2 60 . C a,Caa . PASS . GT 1|2 diff --git a/test/convert.gt.vcf b/test/convert.gt.vcf index 7c719a2a3..18b51eb93 100644 --- a/test/convert.gt.vcf +++ b/test/convert.gt.vcf @@ -1,6 +1,7 @@ ##fileformat=VCFv4.1 ##FILTER= ##FORMAT= +##reference=file://some/path/human_g1k_v37.fasta ##contig= ##bcftools_normVersion=1.2+htslib-1.2.1 ##bcftools_normCommand=norm -m - convert.vcf diff --git a/test/convert.gvcf.out b/test/convert.gvcf.out index 4cd237b85..ff3844c05 100644 --- a/test/convert.gvcf.out +++ b/test/convert.gvcf.out @@ -1,5 +1,6 @@ ##fileformat=VCFv4.1 ##FILTER= +##reference=file://some/path/human_g1k_v37.fasta ##FORMAT= ##FORMAT= ##FORMAT= diff --git a/test/convert.gvcf.vcf b/test/convert.gvcf.vcf index 378edd1e1..61c84732e 100644 --- a/test/convert.gvcf.vcf +++ b/test/convert.gvcf.vcf @@ -1,5 +1,6 @@ ##fileformat=VCFv4.1 ##FILTER= +##reference=file://some/path/human_g1k_v37.fasta ##FORMAT= ##FORMAT= ##FORMAT= diff --git a/test/convert.vcf b/test/convert.vcf index c80278bc7..b2e1b2e0a 100644 --- a/test/convert.vcf +++ b/test/convert.vcf @@ -1,5 +1,6 @@ ##fileformat=VCFv4.1 ##FILTER= +##reference=file://some/path/human_g1k_v37.fasta ##FORMAT= ##FORMAT= ##FORMAT= diff --git a/test/csq.vcf b/test/csq.vcf index b167938c2..49848fec4 100644 --- a/test/csq.vcf +++ b/test/csq.vcf @@ -1,6 +1,7 @@ ##fileformat=VCFv4.2 ##FORMAT= -##INFO= +##reference=file://some/path/human_g1k_v37.fasta +##INFO= ##contig= ##contig= ##contig= diff --git a/test/empty.vcf b/test/empty.vcf index def4e4243..ece43beb3 100644 --- a/test/empty.vcf +++ b/test/empty.vcf @@ -3,4 +3,5 @@ ##contig= ##contig= ##contig= +##reference=file://some/path/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 diff --git a/test/ex2.vcf b/test/ex2.vcf index 17b18962c..e3e8b2b49 100644 --- a/test/ex2.vcf +++ b/test/ex2.vcf @@ -7,14 +7,14 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= -##FORMAT= +##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 14370 rs6054257 G A 29.1 . NS=3;DP=14;AF=0.5;HOMSEQ;DB GT:GQ:DP:HQ:CNL 0|0:48:1:25,30:10,20 1|0:48:8:49,51:. ./.:43:5:.,.:1 20 17330 . T A . q10;s50 NS=3;DP=11;AF=0.017;H2 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:4,5 diff --git a/test/fill-tags.2.out b/test/fill-tags.2.out index 2c06a7a70..750725fe0 100644 --- a/test/fill-tags.2.out +++ b/test/fill-tags.2.out @@ -33,7 +33,7 @@ ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS DP=100223;NS=3;AN=6 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99 +11 2343543 . A . 999 PASS DP=100223;NS=3;AN=6 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 11 5464562 . C T 999 PASS DP=0;NS=0;AN=0;AC=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;NS=3;AN=6;AF=0.833333;MAF=0.166667;AC=5 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;NS=3;AF=0.666667;MAF=0.333333 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0 diff --git a/test/fill-tags.3.out b/test/fill-tags.3.out index 9ee18d388..7d9590f4f 100644 --- a/test/fill-tags.3.out +++ b/test/fill-tags.3.out @@ -32,7 +32,7 @@ ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99 +11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 11 5464562 . C T 999 PASS DP=0;AC_AB=0;AC_BC=0;AC=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;AC_AB=3;AC_BC=4;AC=5 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;AC_AB=2;AC_BC=3 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0 diff --git a/test/filter-missing-floats.vcf b/test/filter-missing-floats.vcf index 8ecd43b60..7a7d57cfb 100644 --- a/test/filter-missing-floats.vcf +++ b/test/filter-missing-floats.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.2 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##contig= ##FORMAT= ##INFO= diff --git a/test/filter.10.out b/test/filter.10.out index 05743909c..64015a62c 100644 --- a/test/filter.10.out +++ b/test/filter.10.out @@ -1,5 +1,6 @@ ##fileformat=VCFv4.1 ##FILTER= +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##contig= ##INFO= ##INFO= diff --git a/test/filter.4.vcf b/test/filter.4.vcf index 78ce13a5c..afe0f4079 100644 --- a/test/filter.4.vcf +++ b/test/filter.4.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.1 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##contig= ##INFO= ##INFO= diff --git a/test/fixref.2.out b/test/fixref.2.out index 08762cb2d..6c1aaac40 100644 --- a/test/fixref.2.out +++ b/test/fixref.2.out @@ -1,5 +1,6 @@ ##fileformat=VCFv4.2 ##FILTER= +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 diff --git a/test/fixref.2a.vcf b/test/fixref.2a.vcf index 313c668fe..cffd1f2e4 100644 --- a/test/fixref.2a.vcf +++ b/test/fixref.2a.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.2 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 diff --git a/test/fixref.2b.vcf b/test/fixref.2b.vcf index 4a346a51a..aaa887d7e 100644 --- a/test/fixref.2b.vcf +++ b/test/fixref.2b.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.2 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO diff --git a/test/fixref.vcf b/test/fixref.vcf index 8ab2a801b..f89c1f226 100644 --- a/test/fixref.vcf +++ b/test/fixref.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.2 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FILTER= ##FORMAT= ##contig= diff --git a/test/gvcf.merge.1.out b/test/gvcf.merge.1.out index bd05d85d2..f9b679d1a 100644 --- a/test/gvcf.merge.1.out +++ b/test/gvcf.merge.1.out @@ -1,10 +1,10 @@ ##fileformat=VCFv4.1 ##FILTER= +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FILTER= ##FILTER= ##FILTER= -##contig= -##contig= +##contig= ##FORMAT= ##FORMAT= ##FORMAT= @@ -22,7 +22,6 @@ ##INFO= ##INFO= ##INFO= -##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G06 D05 H09 chr1 10106 . C . 0 LowGQX BLOCKAVG_min30p3a;AN=2 GT:GQX:DP:DPF ./.:.:.:. 0/0:12:5:0 ./.:.:.:. chr1 10107 . C . 0 LowGQX;HighDPFRatio BLOCKAVG_min30p3a;AN=4 GT:GQX:DP:DPF .:.:0:1 0/0:12:5:0 0/0:5:2:0 diff --git a/test/gvcf.merge.1.vcf b/test/gvcf.merge.1.vcf index 4ea7f0f9b..a83816e52 100644 --- a/test/gvcf.merge.1.vcf +++ b/test/gvcf.merge.1.vcf @@ -1,10 +1,10 @@ ##fileformat=VCFv4.1 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FILTER= ##FILTER= ##FILTER= ##FILTER= -##contig= -##contig= +##contig= ##FORMAT= ##FORMAT= ##FORMAT= diff --git a/test/gvcf.merge.2.vcf b/test/gvcf.merge.2.vcf index bebd0e2f5..b1778efb6 100644 --- a/test/gvcf.merge.2.vcf +++ b/test/gvcf.merge.2.vcf @@ -1,10 +1,10 @@ ##fileformat=VCFv4.1 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FILTER= ##FILTER= ##FILTER= ##FILTER= -##contig= -##contig= +##contig= ##FORMAT= ##FORMAT= ##FORMAT= diff --git a/test/gvcf.merge.3.vcf b/test/gvcf.merge.3.vcf index f79ff117b..bbdc3bb80 100644 --- a/test/gvcf.merge.3.vcf +++ b/test/gvcf.merge.3.vcf @@ -1,10 +1,10 @@ ##fileformat=VCFv4.1 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FILTER= ##FILTER= ##FILTER= ##FILTER= -##contig= -##contig= +##contig= ##FORMAT= ##FORMAT= ##FORMAT= diff --git a/test/idx.vcf b/test/idx.vcf index ba8772dd2..a016206a5 100644 --- a/test/idx.vcf +++ b/test/idx.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.1 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##contig= ##contig= ##contig= diff --git a/test/isec.a.vcf b/test/isec.a.vcf index fe7f87268..1f11c8e96 100644 --- a/test/isec.a.vcf +++ b/test/isec.a.vcf @@ -6,6 +6,10 @@ ##FORMAT= ##FORMAT= ##FILTER= +##contig= +##contig= +##contig= +##contig= ##test= ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta ##INFO= @@ -16,7 +20,7 @@ 1 3062915 . GTTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 1 3106154 . CAAA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 -1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 +1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1,0 GT:GQ:DP 0/1:245:32 1 3157410 . GA G 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21 1 3162006 . GAA G 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30 diff --git a/test/isec.tab.out b/test/isec.tab.out index 1b2e0ed0a..d092d4b2e 100644 --- a/test/isec.tab.out +++ b/test/isec.tab.out @@ -7,21 +7,21 @@ ##FORMAT= ##FORMAT= ##FILTER= +##contig= +##contig= +##contig= +##contig= ##test= ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta ##INFO= ##INFO= ##readme=AAAAAA ##readme=BBBBBB -##contig= -##contig= -##contig= -##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A 1 3062915 . GTTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 1 3106154 . CAAA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 -1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 +1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1,0 GT:GQ:DP 0/1:245:32 1 3157410 . GA G 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21 1 3162006 . GAA G 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30 diff --git a/test/many.alleles.trim.out b/test/many.alleles.trim.out index 7b622e150..e655f993b 100644 --- a/test/many.alleles.trim.out +++ b/test/many.alleles.trim.out @@ -1,5 +1,6 @@ ##fileformat=VCFv4.1 ##FILTER= +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##contig= ##FORMAT= ##INFO= diff --git a/test/many.alleles.vcf b/test/many.alleles.vcf index 491bc89a4..d9b5aa8b8 100644 --- a/test/many.alleles.vcf +++ b/test/many.alleles.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.1 +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##contig= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1528791 diff --git a/test/merge.2.a.vcf b/test/merge.2.a.vcf index c048c0837..c7e081758 100644 --- a/test/merge.2.a.vcf +++ b/test/merge.2.a.vcf @@ -27,4 +27,4 @@ 1 3106154 . C A 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 1 3200010 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 -1 3200020 . C G,T 59.2 PASS AN=4;AC=2 GT:GL ./.:1,2,3,4,5,6 .:1,2,3 +1 3200020 . C G,T 59.2 PASS AN=0;AC=0,0 GT:GL ./.:1,2,3,4,5,6 .:1,2,3 diff --git a/test/merge.2.b.vcf b/test/merge.2.b.vcf index 8700f1c79..4f056fa7b 100644 --- a/test/merge.2.b.vcf +++ b/test/merge.2.b.vcf @@ -26,5 +26,5 @@ 1 3106154 . C CCC 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 1 3106154 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 -1 3200010 . c A,T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 -1 3200020 . C T,G 59.2 PASS AN=4;AC=2 GT:GL ./.:1,4,6,2,5,3 .:1,3,2 +1 3200010 . c A,T 59.2 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:245:32 0/1:245:32 +1 3200020 . C T,G 59.2 PASS AN=0;AC=0,0 GT:GL ./.:1,4,6,2,5,3 .:1,3,2 diff --git a/test/merge.4.a.vcf b/test/merge.4.a.vcf index d7bbd339a..ae3a6f3e4 100644 --- a/test/merge.4.a.vcf +++ b/test/merge.4.a.vcf @@ -29,5 +29,5 @@ 1 3000000 id1 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GQ:XR:XA:XG 0/1:245:0,1:1:0,1,2 0/1:245:1,2:2:0,1,2 1 3000000 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ:XR:XA:XG 0/1:245:1,2:2:0,1,2 0/1:245:2,3:3:1,2,3 1 3000002 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245 -1 3000002 id2 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.:.:. -1 3000002 id3 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:. +1 3000002 id2 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245,0,199:.:.:. 0/1:245,0,199:.:.:. +1 3000002 id3 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245,0,245:.:.:. 0/1:245,0,245:. diff --git a/test/merge.4.out b/test/merge.4.out index 8b69f2b78..b6885f98c 100644 --- a/test/merge.4.out +++ b/test/merge.4.out @@ -30,5 +30,5 @@ 1 3000000 id1 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GQ:XR:XA:XG 0/1:245:0,1,.:1,.:0,1,2,.,.,. 0/1:245:1,2,.:2,.:0,1,2,.,.,. 0/2:245:4,.,5:.,5:3,.,.,4,.,5 0/2:245:6,.,7:.,7:6,.,.,7,.,8 1 3000000 . C CCG,A 59.2 PASS AN=8;AC=2,2 GT:GQ:XR:XA:XG 0/1:245:1,2,.:2,.:0,1,2,.,.,. 0/1:245:2,3,.:3,.:1,2,3,.,.,. 0/2:245:.:.:. 0/2:245:.:.:. 1 3000002 . C CCG,A 59.2 PASS AN=8;AC=2,2 GT:GQ 0/1:245 0/1:245 0/2:245 0/2:245 -1 3000002 id2 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,245,-1.56481e-39,.,.,.:.:.:.:. 0/1:245,-1.56481e-39,1.09706e-28,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:.:.:.:245 -1 3000002 id3 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,245,-1.56481e-39,.,.,.:.:.:.:. 0/1:245,-1.56481e-39,1.09706e-28,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:1,.,2:.,2:1,.,.,2,.,3:245 +1 3000002 id2 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,0,199,.,.,.:.:.:.:. 0/1:245,0,199,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:.:.:.:245 +1 3000002 id3 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,0,245,.,.,.:.:.:.:. 0/1:245,0,245,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:1,.,2:.,2:1,.,.,2,.,3:245 diff --git a/test/merge.gvcf.2.a.vcf b/test/merge.gvcf.2.a.vcf index 4c8cc06b6..55d8b21ce 100644 --- a/test/merge.gvcf.2.a.vcf +++ b/test/merge.gvcf.2.a.vcf @@ -24,7 +24,7 @@ 3 1 . C <*> 0 . END=10;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 1 1619670 . C <*> 0 . END=1619877;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 4 20000975 . C <*> 0 . END=20001070;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 -4 20001071 . T G,<*> 0 . . PL:DP:DV 0,4,10:4:1 +4 20001071 . T G,<*> 0 . . PL:DP:DV 0,4,10,20,30,40:4:1 5 110285 . TAACCCC T . . . PL 89,6,0 5 1110285 . T TAACCCC . . . PL 89,6,0 6 600 . T A . . END=666 PL 66,1,1 diff --git a/test/merge.gvcf.2.out b/test/merge.gvcf.2.out index 1dc0e6389..5a5689863 100644 --- a/test/merge.gvcf.2.out +++ b/test/merge.gvcf.2.out @@ -31,7 +31,7 @@ 1 1619789 . N <*> 0 . END=1619877;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 .:.:. .:.:. 4 20000975 . C <*> 0 . END=20001021;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 .:.:. .:.:. 4 20001022 . C <*> 0 . END=20001070;MinDP=33;QS=1.5,0.5 PL:DP:DV 0,4,10:4:1 0,4,10:4:1 .:.:. -4 20001071 . T G,<*> 0 . QS=0.75,0.25,0 PL:DP:DV 0,4,10:4:1 0,4,10,35,73,113:4:1 .:.:. +4 20001071 . T G,<*> 0 . QS=0.75,0.25,0 PL:DP:DV 0,4,10,20,30,40:4:1 0,4,10,35,73,113:4:1 .:.:. 5 110285 . T C,<*> . . . PL . 114,0,15,35,73,113 . 5 110285 . TAACCCC T . . . PL 89,6,0 . . 5 1110285 . T C,<*> . . . PL . 114,0,15,35,73,113 . diff --git a/test/plugin-missing2ref.out.vcf b/test/plugin-missing2ref.out.vcf index 2e8d1b998..17882db61 100644 --- a/test/plugin-missing2ref.out.vcf +++ b/test/plugin-missing2ref.out.vcf @@ -24,7 +24,7 @@ 1 3000150 . C T 59.2 PASS . GT:GQ 1|1:245 1|1:245 0/1:245 1/1:245 1 3000151 . C T 59.2 PASS . GT:DP:GQ 0|0:32:245 0|0:32:245 0|0:32:245 0|0:32:245 1 3062915 id3D GTTT G 12.9 q10 DP4=1,2,3,4;INDEL;STR=test GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 -1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 2:0,1:409:35:-20,-5,-20 2/2:0,1:409:35:-20,-5,-20 2|2:0,1:409:35:-20,-5,-20 +1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 2:0,1:409:35:-20,-5,-20 2/2:0,1:409:35:-20,-5,-20,-20,-5,-20 2|2:0,1:409:35:-20,-5,-20,-20,-5,-20 2 3199812 . G GTT,GT 82.7 PASS . GT:GQ:DP 0|0:322:26 0|0:322:26 0|0:322:26 0|0:322:26 3 3212016 . CTT C,CT 79 PASS . GT:GQ:DP 0|0:91:26 0|0:91:26 0|0:91:26 0|0:91:26 4 3258448 . TACACACAC T 59.9 PASS . GT:GQ:DP 0|0:325:31 0|0:325:31 0|0:325:31 0|0:325:31 diff --git a/test/regions.vcf b/test/regions.vcf index d5613c101..595d838fb 100644 --- a/test/regions.vcf +++ b/test/regions.vcf @@ -17,13 +17,13 @@ 1 3062915 . GTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 1 3106154 . CA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 -1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 +1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1,0 GT:GQ:DP 0/1:245:32 1 3157410 . G A 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21 1 3162006 . G A 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30 -1 3184885 . T TA 246 PASS DP=10;AN=2;AC=1,1 GT:GQ:DP 1/2:12:10 -2 3199812 . G T 481 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:322:26 -2 3199815 . C T 481 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:322:26 -3 3212016 . C A 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26 -3 3212026 . C A 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26 -3 3212036 . C A 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26 +1 3184885 . T TA 246 PASS DP=10;AN=2;AC=1 GT:GQ:DP 1/2:12:10 +2 3199812 . G T 481 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:322:26 +2 3199815 . C T 481 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:322:26 +3 3212016 . C A 565 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:91:26 +3 3212026 . C A 565 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:91:26 +3 3212036 . C A 565 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:91:26 diff --git a/test/view.10.out b/test/view.10.out index 9ef4bcef4..a4d58ef7a 100644 --- a/test/view.10.out +++ b/test/view.10.out @@ -30,7 +30,7 @@ ##FILTER= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99 +11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. X 3048719 . T C 999 PASS DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 0|1:255,0,157:52:99 Y 8657215 . C A 999 PASS DP4=74915,114274,1948,2955;DP=195469;Dels=0;FS=3.181;MQ0=0;MQ=50;PV4=0.86,1,0,1;QD=33.77;AN=2;AC=1 GT:PL:DP:GQ 0:0,255:47:99 1:255,0:64:99 .:.:.:. diff --git a/test/view.6.out b/test/view.6.out index f0d6d7546..3a2b14d62 100644 --- a/test/view.6.out +++ b/test/view.6.out @@ -30,7 +30,7 @@ ##FILTER= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99 +11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0 diff --git a/test/view.GL.vcf b/test/view.GL.vcf index 6b8de7010..b51ecae92 100644 --- a/test/view.GL.vcf +++ b/test/view.GL.vcf @@ -12,7 +12,7 @@ ##FILTER= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS . GL 0,-25.5,-25.5 0,-25.5,-25.5 0,-25.5,-25.5 +11 2343543 . A . 999 PASS . GL 0 0 0 11 5464562 . C T 999 PASS . GL 0,0,0 0,0,0 0,0,0 20 76962 rs6111385 T C 999 PASS . GL -25.5,0,-25.5 -25.5,-25.5,0 -25.5,-25.5,0 20 126310 . ACC A 999 StrandBias;EndDistBias . GL -25.5,0,-13.2 -25.5,0,-13.9 -25.5,-21.3,0 diff --git a/test/view.GTsubset.NA1NA2NA3.out b/test/view.GTsubset.NA1NA2NA3.out index 7fbb27e0c..097fdbf63 100644 --- a/test/view.GTsubset.NA1NA2NA3.out +++ b/test/view.GTsubset.NA1NA2NA3.out @@ -30,7 +30,7 @@ ##FILTER= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99 +11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. 20 326891 . A AC 999 PASS DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2 GT:DP:GQ:PL 0|1:117:99:255,0,132 0|1:111:99:255,0,139 ./.:.:.:.,.,. Y 10011673 rs78249411 G A 999 MinAB DP4=47351,30839,178796,279653;DP=550762;Dels=0;FS=41.028;MQ0=37362;MQ=26;PV4=0,0,0,1;QD=17.45;AN=2;AC=2 GT:PL:DP:GQ 1:126,101:146:37 1:95,0:130:99 .:.:.:. diff --git a/test/view.PL.vcf b/test/view.PL.vcf index 2d743b96c..db1f11402 100644 --- a/test/view.PL.vcf +++ b/test/view.PL.vcf @@ -12,7 +12,7 @@ ##FILTER= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS . PL 0,255,255 0,255,255 0,255,255 +11 2343543 . A . 999 PASS . PL 0 0 0 11 5464562 . C T 999 PASS . PL 0,0,0 0,0,0 0,0,0 20 76962 rs6111385 T C 999 PASS . PL 255,0,255 255,255,0 255,255,0 20 126310 . ACC A 999 StrandBias;EndDistBias . PL 255,0,132 255,0,139 255,213,0 diff --git a/test/view.exclude.out b/test/view.exclude.out index 324c32066..853c3c28f 100644 --- a/test/view.exclude.out +++ b/test/view.exclude.out @@ -30,7 +30,7 @@ ##FILTER= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 -11 2343543 . A . 999 PASS DP=100223;AN=4 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 +11 2343543 . A . 999 PASS DP=100223;AN=4 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 11 5464562 . C T 999 PASS DP=0;AC=0;AN=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;AC=3;AN=4 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 diff --git a/test/view.vcf b/test/view.vcf index 9e6c2fdb0..cb35ad2d5 100644 --- a/test/view.vcf +++ b/test/view.vcf @@ -29,7 +29,7 @@ ##FILTER= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99 +11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0