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ChaissonLab / vamos

VNTR annotation using motif selection
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Issues with the output vcf file #11

Open ghzhaole opened 2 months ago

ghzhaole commented 2 months ago

Hi there,

I tried to run vamos on a long-read BAM file, with the following command: ./vamos --read -b HG002.target.bam -r target_region.bed -s HG002 -o HG002.chr1.vcf

When getting the output file, I found something strange in my VCF file: image

The motif compositions showed in ALTANNO_H1 and ALTANNO_H2 are palindromic sequences. And the same situation was found in all VNTR loci.

Is there something wrong with my procedure or long-read data? Thanks for your help!

mchaisso commented 2 months ago

Strange, we can't replicate this with our own HG002 data. Can you provide a small bam (just over this pos at 241614676) and the region file you are using?

Running on a HG002 HiFi bam, just chromosome 10, I can pull out a quick example: chr10 114254 . N . PASS END=114318;RU=CTTC,CTTT,TTTC,CTTTC,CTTCC;SVTYPE=VNTR;ALTANNO_H1=3,1,1,2,0,0,0,0,4,3,3,1,0,1,1,1;LEN_H1=16;ALTANNO_H2=3,1,1,2,0,0,0,0,4,3,3,1,0,1,1;LEN_H2=15; GT 1/2