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How to do variant calling on .sam and .bam files using 'bio-samtools'?

How to do variant calling on .sam files using 'bio-samtools'?

I have the code:

#!/usr/bin/ruby

require 'bio-samtools'

bam = Bio::DB::Sam.new(:bam=>"my_sorted.bam", :fasta=>'ref.fasta')
  bam.open

What methods to call on bam object or what next steps to do? Thank you.

wgs sequencing sequence software-error
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updated by kojix2 kojix2 • written by elvissober • elvissober

Need all in one Ruby workflow, thank you for you replies

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written by elvissober • elvissober

3 answers

Have you read the github page?

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written by andrew.j.skelton73 andrew.j.skelton73

Looks like you'll want to call mpileup with the :g option. Documentation and code are here:

https://github.com/helios/bioruby-samtools/blob/fe97402bf150877f0d84587abc82fab35d66297c/lib/bio/db/sam.rb#L186

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updated by Ram Ram • written by Sean Davis Sean Davis

I've created ruby-htslib to make this sort of thing possible. It's not as well tested as the fine libraries in Python and other languages, so there may be some bugs left, but if you find a bug, I'll fix it.

https://github.com/kojix2/ruby-htslib

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written by kojix2 kojix2

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