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Revision as of 15:37, 10 September 2013
, 15:37, 10 September 2013→Producing pileups of sequence reads at variant sites
For example, you can modify from the following command
For example, you can modify from the following command
/net/fantasia/home/hmkang/bin/captTest/bin/capt-pileup --index /net/1000g/hmkang/1KG/phase3/index/20130502.gotcloud.low_coverage.2col.index --out /net/1000g/hmkang/1KG/phase3/wg.consensus/lcmpus/phase3.low_coverage.wgs --loci /net/1000g/hmkang/1KG/phase3/wg.consensus/union/union.snps.sites.loci --mosix-nodes 10,11,12,13 --ref /net/1000g/hmkang/1KG/phase3/gotcloud/gotcloud.ref/hs37d5.fa --clip-overlap
/net/fantasia/home/hmkang/bin/captTest/bin/capt-pileup --index /net/1000g/hmkang/1KG/phase3/index/20130502.gotcloud.low_coverage.2col.index \\
--out /net/1000g/hmkang/1KG/phase3/wg.consensus/lcmpus/phase3.low_coverage.wgs \\
--loci /net/1000g/hmkang/1KG/phase3/wg.consensus/union/union.snps.sites.loci \\
--mosix-nodes 10,11,12,13 \\
--ref /net/1000g/hmkang/1KG/phase3/gotcloud/gotcloud.ref/hs37d5.fa \\
--clip-overlap
Have a peek of the each input file to better understand what you actually need to prepare
Have a peek of the each input file to better understand what you actually need to prepare
