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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.

How to Run

Important Filters