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Revision as of 13:35, 10 March 2010
, 13:35, 10 March 2010→(3) Build a list of individuals within each population
== (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 ==
/home/ylwtx/codes/cpp/mach-1.0.16/test_thunder/2009.11.all
/home/ylwtx/codes/cpp/mach-1.0.16/test_thunder/2009.11.all
STEP 0 in s1-5.csh
STEP 0 in s1-5.csh
Note: Check to make sure that all the individuals with GLF are included in the list “NA.number.by.popn”
Note: Check to make sure that all the individuals with GLF are included in the list “NA.number.by.popn”
== (4) Link files and tabulate # of files per population, per platform ==
== (4) Link files and tabulate # of files per population, per platform ==
