How to do variant calling on .sam and .bam files using 'bio-samtools'?
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5.5 years ago
elvissober ▴ 20

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.

 

software error sequencing sequence wgs • 1.3k views
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why not using a simple shell script ?

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

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5.5 years ago

Have you read the github page?

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5.5 years ago

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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