212
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search1000 Genomes Project Pilot 1 SNP Calling (view source)
Revision as of 13:34, 10 March 2010
, 13:34, 10 March 2010→(2) Split GLF files by chromosome
== (2) Split GLF files by chromosome ==
== (2) Split GLF files by chromosome ==
/home1/ylwtx/2009.08.GLF-split/
/home1/ylwtx/2009.08.GLF-split/
update-glf.csh<br>splitGLF.csh
update-glf.csh<br>splitGLF.csh
key command: glfSplit<br>Source codes: ~goncalo/code/glfSplit/
key command: glfSplit<br>Source codes: ~goncalo/code/glfSplit/
Input GLF format: gz or bgzf<br>Output GLF format: gz
Input GLF format: gz or bgzf<br>Output GLF format: gz
Tom suggested combing the first two steps using the following samtools command:<br>samtools -view -u *.bam 22 | samtools pileup –g - > *.glf
Tom suggested combing the first two steps using the following samtools command:<br>samtools -view -u *.bam 22 | samtools pileup –g - > *.glf
== (3) Build a list of individuals within each population ==
== (3) Build a list of individuals within each population ==
