Difference between revisions of "Thunder"

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(Created page with 'This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. == Input Data == To get started, you will need bam files in…')
 
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== Input Data ==
 
== Input Data ==
  
To get started, you will need bam files in the standard format [http://samtools.sourceforge.net/SAM1.pdf bam format].
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To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format].
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If you do not have glf files, you can generate them from bam files (bam format also specified in [http://samtools.sourceforge.net/SAM1.pdf glf format bam format]) using the following command line:
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  samtools pileup -g -T 1 -f ref.fa my.bam > my.glf
  
 
== How to Run ==
 
== How to Run ==
  
 
== Important Filters ==
 
== Important Filters ==

Revision as of 12:32, 15 October 2010

This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder.

Input Data

To get started, you will need glf files in the standard format glf format.

If you do not have glf files, you can generate them from bam files (bam format also specified in glf format bam format) using the following command line:

 samtools pileup -g -T 1 -f ref.fa my.bam > my.glf

How to Run

Important Filters