Var
Format
cg sv ?options? bamfile ?resultfile?
Summary
generic command to call structural variants based on the alignment
in bamfile.
Description
The command can be used to call structural variants using
different methods. The methods are implemented in separate commands
such as cg sv_manta; The -method options determines which one is
used. The resultfile is a tsv file containing the called
structural variants. If ""resultfile is not given, a
file name will be derived from the bam file name: If the bamfile has
a name of the form map-alignmethod-sample.bam, the result file will
will be var-svcaller-alignmethod-sample.tsv.zst. Other result files
may also be created, depending on the method used.
cg sv can distribute structural variant calling by analysing
separate regions in parallel and combining the results (-distrreg
option). This command can be distributed on a cluster or using
multiple cores with job options (more
info with cg help joboptions)
Arguments
- bamfile
- alignment on which to call variants
- resultfile
- filename of the resulting structural variant calls
Options
- -method svcaller
- use the given method (svcaller) to call structural
variants. Default svcaller is manta. Possible values are: manta,
lumpy sniffles, npinv, cg, gridds
- -refseq refseq
- genomic reference sequence
- -regionfile regionfile
- only call variants in the region(s) given in regionfile
- -regmincoverage mincoverage
- If no regionfile is given, variants will be called only in
regions with a coverage of at least mincoverage (default 3)
- -distrreg
- distribute regions for parallel processing (default
s50000000). Possible options are 0: no distribution (also
empty) 1: default distribution (s50000000) schr or
schromosome: each chromosome processed separately chr or
chromosome: each chromosome processed separately, except the
unsorted, etc. with a _ in the name that will be combined), a
number: distribution into regions of this size a number
preceded by an s: distribution into regions targeting the given
size, but breaks can only occur in unsequenced regions of the
genome (N stretches) a number preceded by an r: distribution
into regions targeting the given size, but breaks can only occur in
large (>=100000 bases) repeat regions a number preceded by
an g: distribution into regions targeting the given size, but
breaks can only occur in large (>=200000 bases) regions without
known genes a filename: the regions in the file will be used
for distribution
- -split 1/0
- indicate if in the datafiles, multiple alternative genotypes
are split over different lines (default 1)
- -t number (-threads)
- number of threads used by each job (if the method supports
threads)
- -cleanup 0/1
- Use 0 to no cleanup some of the temporary files (vcf, delvar,
...)
Category
Variants