Genomecomb moved to github on https://github.com/derijkp/genomecomb
with documentation on https://derijkp.github.io/genomecomb.
For up to date versions, go there. These pages only remain here for the data on the older scientific
application (or if someone really needs a long obsolete version of the software)
Regextract
Format
cg regextract ?options? file1 ?file2? ...
Summary
Find regions with a minimum or maximum coverage in a bam, bcol or
tsv file.
Description
Write a regionsfile to stdout that contains all regions in the
given bam, bcol or tsv file(s) that have given minimum or maximum
coverage. e.g. regions in file1 with a minimum coverage of 20 are
extracted using
cg regextract -min 20 file1
Using the -max option will give all regions where the coverage in
the file reaches at most the given maximum. WARNING: This will only
check regions that have a actual given coverage in the file;
Positions that are not present in the given file are not returned!
For bam files (only), you can use the -all option to include these
regions with no given coverage (in this case unused reference
sequences).
If there is no chromosome data in the input files (tsv without
chromosome), the chromosome name is taken from the filename by
splitting on "-", and taking the second element.
Arguments
- file1
- file containing (chromosome,) position and value columns, or
bcol file.
- ...
- other files
Options
- -qfields list
- list (separated by spaces) of possible fieldnames to use as
values for the cutoff; The first in the list that is in the header
will be used (default = "coverage
uniqueSequenceCoverage"). This option is not used for bcol
files, as they contain data for only one "column".
- -posfields list
- list (separated by spaces) of possible fieldnames to use as
position; The first in the list that is in the header will be used
(default = "offset pos position begin start"). This
option is not used for bcol files.
- -min number
- extract regions with coverage >= number.
- -max number
- extract regions with coverage <= number.
- -shift
- change the position by the given amount, e.g. -1 to change
from 1-based to 0-based coordinates
- -q number
- Minimum mapping quality for an alignment to be used (only
used for bams)
- -Q number
- Minimum base quality for a base to be considered (only used
for bams)
- -f 0/1 (--filtered)
- (only used for bams) if 1, skip anomalous read pairs and low
quality for calculating depth. Low quality filtering in this option
is achieved by setting -q and -Q at 20, unless you specifically
define other values for these options. (default 0)
- -all 0/1
- (only for bams) Return all regions (<= max), including
regions with no given coverage (unused reference sequences)
Category
Regions
