zeeev
commented
6 years ago Hi @ivangalvan,
Whamg doesn't genotype SVs. However, you can genotype these events with: https://github.com/hall-lab/svtyper
Best,
Zev
Closed ivangalvan closed 6 years ago
zeeev
commented
6 years ago Hi @ivangalvan,
Whamg doesn't genotype SVs. However, you can genotype these events with: https://github.com/hall-lab/svtyper
Best,
Zev
Hi Zev,
I have installed the last version of wham available from: http://zeeev.github.io/wham/
When I run wham, all the detected variants have missing genotypes. I run the same bam file with other variant callers (GATK, deepvariant, manta, freebayes, etc) and all of them generate genotypes.
See, please, the commands and outputs below, I made something wrong?
Thank you,
Ivan
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command:
whamg -x 48 -a human_ref_bwa_0.7.5a/hg19.fa -f insilico15_all_tumor.markdups.bam > wham/insilico_2/insilico2_tumor.vcf 2> wham/insilico_2/insilico2_tumor.err
head output /insilico2_tumor.vcf:
fileformat=VCFv4.2
source=WHAM-GRAPHENING:v1.7.0-311-g4e8c
reference=human_ref_bwa_0.7.5a/hg19.fa
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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT insil
1 7570071 . A
. PASS A=11;CIEND=-10,10;CIPOS=-10,10;CF=1;CW=0.727273,0.272727,0,0,0;D=8;DI=395.75;END=7571511;EV=0;I=0;SR=3;SS=0;SVLEN=-1440;SVTYPE=DEL;T=0;TAGS=insil;TF=5;U=3;V=0 GT:DP:SP .:.:10 1 8180881 . A . PASS A=45;CIEND=-10,10;CIPOS=-10,10;CF=1;CW=0.355556,0.577778,0,0.0666667,0;D=16;DI=0;END=47694139;EV=6;I=3;SR=20;SS=0;SVLEN=39513258;SVTYPE=DUP;T=0;TAGS=insil;TF=6;U=26;V=0 GT:DP:SP .:.:42
1 8381454 . A . PASS A=13;CIEND=-10,10;CIPOS=-10,10;CF=0;CW=0,0.0769231,0,0.923077,0;D=0;DI=0;END=8381454;EV=0;I=12;SR=1;SS=0;SVLEN=20;SVTYPE=INS;T=0;TAGS=insil;TF=0;U=1;V=0 GT:DP:SP .:.:20