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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Bcftools minimal support reads #574

Closed sunliang3361 closed 7 years ago

sunliang3361 commented 7 years ago

Hi, what is the default minimal support reads for bcftools to call a snp/indel? I found that there is an indel in my sample with two support reads, it seems that bcftools will not consider it as an indel. Is there any parameter I can set up for the minimal support reads (such as varscan)? Thanks

pd3 commented 7 years ago

This is in the mpileup part, check the -F, -m and -p options.