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Revision as of 15:52, 10 September 2013
, 15:52, 10 September 2013→Producing pileups of sequence reads at variant sites
capt pileup [options]
capt pileup [options]
Required Options (Run epacts single -man or see wiki for more info):
Required Options (Run capt-pileup -man or see wiki for more info):
-loci STR Input genomic position to perform pileup
-loci STR Input genomic position to perform pileup
-index STR Index file containing sample IDs and BAM file path
-index STR Index file containing sample IDs and BAM file path
* 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
Internally, the current implementation runs samtools to collect this pileup. We have a separate software package that handles indels and SNPs together and will replace samtools soon.
Examples from the 1000 Genomes project is available at
Examples from the 1000 Genomes project is available at
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
HG00107 /net/1000g/1000g/data/HG00107/alignment/HG00107.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.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
$ head /net/1000g/hmkang/1KG/phase3/wg.consensus/union/union.snps.sites.loci
1 10002
1 10002
1 10004
1 10004
1 10473
1 10473
1 10478
1 10478
The output file has a bit cryptic format, but it will be readable to the downstream software. See [[http://samtools.sourceforge.net/pileup.shtml Samtools Pileup Format]] web page to understand the details of the output format.
$ zcat /net/1000g/hmkang/1KG/phase3/wg.consensus/lcmpus/phase3.low_coverage.wgs.HG00096.txt.gz | head
1 10327 T 4 ,.,. E@,H >>>F 76,30,36,18
1 10469 C 5 .g,$,. A?/;P >>>FF 78,66,100,38,12
1 10470 G 4 .,,. 8?CH >>FF 79,67,39,13
1 10471 C 4 .,,. D=:Q >>FF 80,68,40,14
1 10472 G 4 .,,. <DLH >>FF 81,69,41,15
1 10473 G 4 .,,. C=DR >>FF 82,70,42,16
1 10478 C 5 .,,., DJQR> >>FF> 87,75,47,21,2
1 10492 C 5 ,,T,, QKAA@ >FF>> 89,61,35,16,7
1 10494 G 5 ,,.,, QQ<G> >FF>> 91,63,37,18,9
1 10503 T 5 ,$,.,, /QDAG >FF>> 100,72,46,27,18
(TO BE CONTINUED)..
