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bcftools differs in depth from IGV and samtools
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
bcftools (top) and samtools (bottom)
samtools read out
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