Thunder
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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
