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Revision as of 15:36, 10 September 2013
, 15:36, 10 September 2013→Producing pileups of sequence reads at variant sites
* Overlapping pair of read fragments are not specially handled by default. **It is recommended** to explicitly turn on --clip-overlap option to clip either side of overlapping read fragment to improve the filtering performance.
* Overlapping pair of read fragments are not specially handled by default. **It is recommended** to explicitly turn on --clip-overlap option to clip either side of overlapping read fragment to improve the filtering performance.
* By default, it assume that it runs in one machine. If you are running in MOSIX enable cluster, mosix-nodes [node1,node2,node3,..,noden] will allow to spread the jobs to multiple nodes in parallel
* By default, it assume that it runs in one machine. If you are running in MOSIX enable cluster, mosix-nodes [node1,node2,node3,..,noden] will allow to spread the jobs to multiple nodes in parallel
Examples from the 1000 Genomes project is available at
cat /net/1000g/hmkang/1KG/phase3/scripts/m02-create-pileups.sh
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
Have a peek of the each input file to better understand what you actually need to prepare
$ head /net/1000g/hmkang/1KG/phase3/index/20130502.gotcloud.low_coverage.2col.index
HG00096 /net/1000g/1000g/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
HG00097 /net/1000g/1000g/data/HG00097/alignment/HG00097.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
HG00099 /net/1000g/1000g/data/HG00099/alignment/HG00099.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
HG00100 /net/1000g/1000g/data/HG00100/alignment/HG00100.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
HG00101 /net/1000g/1000g/data/HG00101/alignment/HG00101.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
HG00102 /net/1000g/1000g/data/HG00102/alignment/HG00102.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
HG00103 /net/1000g/1000g/data/HG00103/alignment/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
HG00105 /net/1000g/1000g/data/HG00105/alignment/HG00105.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
HG00106 /net/1000g/1000g/data/HG00106/alignment/HG00106.mapped.ILLUMINA.bwa.GBR.low_coverage.20121211.bam
HG00107 /net/1000g/1000g/data/HG00107/alignment/HG00107.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
$head /net/1000g/hmkang/1KG/phase3/wg.consensus/union/union.snps.sites.loci
1 10002
1 10004
1 10005
1 10327
1 10469
1 10470
1 10471
1 10472
1 10473
1 10478
