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lh3 / minipileup

Simple pileup-based variant caller
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Enhancement request: adding the command call to the VCF header #3

Closed jelber2 closed 6 months ago

jelber2 commented 6 months ago

When you have time, might it be possible to add the command call to the VCF header?

I am not sure what the VCF spec says about the format

EDIT: I realized you did have the version at the top of the VCF header

call:minipileup -vcC -q30 -Q20 -a 2 -s 5 -f ../Homo_sapiens_GRCh38_no_alt.fa -r chr1:1-248956422 herro/hg002.herro.Q30.sam1.3.SoftClip.bam

I could submit a pull request, but I unfortunately am quite unsure about the format to add. EDIT from BCFtools, I see something such as in the header ##bcftools_concatCommand=concat -a -O z -o /tmp/tmpw6n7FQ.vcf.gz /tmp/input.chr1:1-2712601lACuYT.prep.vcf.gz