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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.Leave a comment:
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Getting FQ from bcftools 1.2
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:
Code: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
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