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How to run VCFTools and other variant callers on a set of .sam output of BBMap and other aligners?

How to run VCFTools and other variant callers on .sam outputs of BBMap and other aligners? Need a clear example in Unix shell and from Python subprocess and Java/Ruby, please. Thank you.

soft wgs sequencing vcf sam
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written by elvissober • elvissober

1 answer

  1. VCFtools doesn't call variants
  2. Each caller gives example on its page. You will more or less never find examples from within python/java/ruby. Once you know what to type at the command line those will be obvious.
  3. You want to use a sorted BAM file, not a SAM file.
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written by Devon Ryan Devon Ryan

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