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bcftools differs in depth from IGV and samtools

Open robertzeibich opened this issue 1 year ago • 3 comments

I would like to evaluate the performance of different variant callers based on the BAM file.

I tried samtools, but with samtools, I do not get information on strand bias, etc. Therefore, I want to use bcftools.

However, when I use bcftools, I notice that there is a difference in depth/coverage between IGV, samtools and bcftools:

IGV screenshot image

bcftools (top) and samtools (bottom) image

samtools read out image

How can I get the same/similar numbers, especially to IGV with bcftools? Help would be much appreciated.

Current command: bcftools mpileup /scratch/xm41/ct/bams/GRMH019.bam -f /scratch/xm41/hg38_resources/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -r chr1:122519382-122519382 -A -Q 0 --ff UNMAP,DUP -a FORMAT/ADF,FORMAT/ADR

bcftools version: 1.14

robertzeibich avatar Dec 07 '22 06:12 robertzeibich