Question: How to do variant calling on .sam and .bam files using 'bio-samtools'?
0
gravatar for elvissober
3.8 years ago by
elvissober20
South Africa
elvissober20 wrote:

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.

 

ADD COMMENTlink modified 3.8 years ago by Sean Davis25k • written 3.8 years ago by elvissober20

why not using a simple shell script ?

ADD REPLYlink written 3.8 years ago by Pierre Lindenbaum123k

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

ADD REPLYlink written 3.8 years ago by elvissober20
0
gravatar for andrew.j.skelton73
3.8 years ago by
London
andrew.j.skelton735.8k wrote:

Have you read the github page?

ADD COMMENTlink written 3.8 years ago by andrew.j.skelton735.8k
0
gravatar for Sean Davis
3.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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

 

ADD COMMENTlink written 3.8 years ago by Sean Davis25k
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