Entering edit mode
5.2 years ago
fwuffy ▴ 100
Hi- Can someone help me identify these PL (phred likelihood) genotype values for this multi-allelic indel row in a VCF?
The VCF row:
chr1 36418926 . caagaaa cAAAAaagaaa,caa,cAAaagaaa 9.95049 . INDEL;IDV=4;IMF=0.666667;DP=6;VDB=0.0340507;SGB=-0.556411;MQSB=1;MQ0F=0;AF1=0.502508;AC1=1;DP4=1,0,3,1;MQ=59;FQ=-14.6836;PV4=1,1,0.342519,1 GT:PL:DP 0/1:72,25,45,27,0,47,40,13,15,59:5
With 3 alt alleles, I expect 6 values, not 10
A/A:72, A/B:25, B/B:45, A/C: 27, B/C: 0, C/C: 47, ??: 40, ??: 13, ??: 15, ??: 59
These are unphased, one sample. called with bcftools 1.6+htslib-1.6 Using this to call variants:
samtools mpileup -v -u -B -t DP -f full.fa mapped-sorted-mkdup.bam | bcftools call -c -v - > germline-variants-all.vcf
Oh right!!! Duh. It's been a while...
so I'd have
The coverage is low cause it's a sub-sampled fastq. I also know there are issues around indels but just for the sake of knowing what i'm supposed to be looking at, setting aside the correctness of it for now.
*edit: This also confuses me cause the genotype call is 0/1.