User:Lindenb/Notebook/UMR915/20101125

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20101124        Top        20101126       


Dindel

Running Dindel on individual1.

script so far:
DINDEL_DIR=/usr/local/package/dindel-1.01
HG18=/GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa
BAM=XXXXXXXXXXXXXXXXXXXXXXXXXXXX.bam

stage1:
	${DINDEL_DIR}/binaries/dindel-1.01-linux-64bit --analysis getCIGARindels --bamFile ${BAM} --outputFile sample.dindel_output --ref ${HG18}
stage2:
	python ${DINDEL_DIR}/dindel-1.01-python/makeWindows.py --inputVarFile sample.dindel_output.variants.txt --windowFilePrefix sample.realign_windows --numWindowsPerFile 1000

stage3:
	for I in `ls sample.realign_windows.*.txt | cut -d '.' -f 3`; do ${DINDEL_DIR}/binaries/dindel-1.01-linux-64bit --analysis indels --doDiploid --bamFile ${BAM}  --outputFile sample.dindel_stage2_output_windows.$$I  --ref ${HG18} --varFile sample.realign_windows.$$I.txt --libFile sample.dindel_output.libraries.txt ; done


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