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Old 06-18-2015, 01:04 AM   #2
Samtools maintainer
Location: Cambridge, UK

Join Date: Jul 2009
Posts: 39

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.
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