GenomeComb

Process_sv

Format

cg process_sv ?options? cgdir resultdir dbdir

Summary

Do all steps on a Complete Genomics sample to generate structural variant calls

Description

cg process_sv detects structural variants based on discordant read pairs in the Complete Genomics (CGI) mapping files. This structural variant caller was developed on some of the earliest Complete Genomics samples, and has become a bit superfluous since Complete Genomics includes structural variant calls in their standard output. There are some reasons that it may stil be useful:

cg process_sv successively runs the following steps:

Arguments

cgdir
directory conataing the CGI mapping files
resultdir
"sample directory" where results will be written. The resultfile will be named sv-samplename.tsv (where samplename is the name of the resultdir). All intermediate data is stored in a subdir sv in resultdir
dbdir
directory containing reference data (genome sequence, annotation, ...).

Options

-force 0/1
force full reanalysis even if some files already exist

supports job options (more info with cg help joboptions):

-d number
distribute subjobs of command over number processes
-d sge
use grid engine to distribute subjobs

Resultfile

Example

cg process_sv GS27657-FS3-L01 NA19238cg /complgen/refseq/hg19

Category

Structural variants