Getting FQ from bcftools 1.2

[Greg_owens]

I'm using samtools and bcftools to call hapmap snps from WGS data. With the older version of samtools the vcf file included FQ per site, but when I use the latest version (samtools/bcftools 1.2) it doesn't. I need FQ for a downstream program, so is there a way to force bcftools to output it?

Here's what my code looks like now:

samtools mpileup -ugf hg19.fasta -l annotHapMap2L.txt $bam/$name.bam | bcftools call -mO v -o $vcf/$name.HM.vcf -V indels -P 0.5

[jmarshall]

Current bcftools 1.x contains two calling methods: call -c is the original bcftools consensus caller, while call -m is a more recent multi-allelic caller. Only the consensus caller outputs FQ.

If your downstream program is expecting to get old-bcftools-style input, you probably want to be using call -c.

[Greg_owens]

That works. Thanks!