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Old 08-23-2021, 01:24 PM   #2
Location: san francisco

Join Date: Jul 2010
Posts: 16

Brian Knaus, on his vcfR Git site, helped me figure this out. Turns out if you want to include Hardy Weinberg in your population variant calling with bcftools, you must include some annotations with the -a option for bcftools mpileup. Any annotations not listed with -a will not be included in the 'gt' slot; they will be in the 'info' slot so "" will ignore any annotations not in the 'gt' slot. Alternatively, you can try '', but that did not pull DP stats for each individual for me.

The bcftools commands that solved the above issue was:

"bcftools mpileup -Ou -I -B -C 50 -a QS -a AD -a DP --threads $THREADS -f $REF $bam_files"
call_cmd="bcftools call -mv -Oz --threads $THREADS -o $OUTFILE"
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