Thunder: Difference between revisions
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samtools pileup -g -T 1 -f ref.fa my.bam > my.glf | samtools pileup -g -T 1 -f ref.fa my.bam > my.glf | ||
Note: you will need the reference fasta file ref.fa to create glf file from bam file. | |||
== 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
Note: you will need the reference fasta file ref.fa to create glf file from bam file.
