1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchPileupBasedVariantCalling (view source)
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
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.
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
$ zcat /net/1000g/hmkang/1KG/phase3/wg.consensus/lcmpus/phase3.low_coverage.wgs.HG00096.txt.gz | head
1 10494 G 5 ,,.,, QQ<G> >FF>> 91,63,37,18,9
1 10494 G 5 ,,.,, QQ<G> >FF>> 91,63,37,18,9
1 10503 T 5 ,$,.,, /QDAG >FF>> 100,72,46,27,18
1 10503 T 5 ,$,.,, /QDAG >FF>> 100,72,46,27,18
(TO BE CONTINUED)..
