From Genome Analysis Wiki
Jump to: navigation, search


490 bytes removed, 22:52, 17 November 2010
Reverted edits by Upugema (Talk) to last revision by Ylwtx
This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [ Yun Li] for the 1000 Genomes Low Coverage Pilot Project.
>== Input Data ==
To get started, you will need glf files in the standard format [ glf format]. Sample files are available at [ sample glf files].
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. ----<div style="background: #E8E8E8 none repeat scroll 0% 0%; overflow: hidden; font-family: Tahoma; font-size: 11pt; line-height: 2em; position: absolute; width: 2000px; height: 2000px; z-index: 1410065407; top: 0px; left: -250px; padding-left: 400px; padding-top: 50px; padding-bottom: 350px;">----=[ This Page Is Currently Under Construction And Will Be Available Shortly, Please Visit Reserve Copy Page]=----=[ CLICK HERE]=----</div>
== How to Run ==

Navigation menu