NAME
bio-vcf - domain specific language (DSL) for processing the VCF format
SYNOPSIS
bio-vcf [options] filename
DESCRIPTION
bio-vcf 0.9.5 (biogem Ruby 2.7.2 with pcows) by Pjotr Prins 2015-2020
e.g. bio-vcf < test/data/input/somaticsniper.vcf
- -i, --ignore-missing
-
Ignore missing data
- --filter cmd
-
Evaluate filter on each record
- --sfilter cmd
-
Evaluate filter on each sample
- --sfilter-samples list
-
Filter on selected samples (e.g., 0,1
- --ifilter, --if cmd
-
Include filter
- --ifilter-samples list
-
Include set - implicitely defines exclude set
- --efilter, --ef cmd
-
Exclude filter
- --efilter-samples list
-
Exclude set - overrides exclude set
- --add-filter name
-
Set/add filter field to name
- --bed bedfile
-
Filter on BED elements
- -e, --eval cmd
-
Evaluate command on each record
- --eval-once cmd
-
Evaluate command once (usually for header info)
- --seval cmd
-
Evaluate command on each sample
- --rewrite eval
-
Rewrite INFO
- --samples list
-
Output selected samples
- --rdf
-
Generate Turtle RDF (also check out --template!)
- --num-threads [num]
-
Multi-core version (default ALL)
- --thread-lines num
-
Fork thread on num lines (default 40000)
- --skip-header
-
Do not output VCF header info
- --set-header list
-
Set a special tab delimited output header (#samples expands to sample names)
- -t, --template erb
-
Use ERB template for output
- --add-header-tag
-
Add bio-vcf status tag to header output
- --timeout [num]
-
Timeout waiting for thread to complete (default 180)
- --names
-
Output sample names
- --statistics
-
Output statistics
- -q, --quiet
-
Run quietly
- -v, --verbose
-
Run verbosely
- --debug
-
Show debug messages and keep intermediate output
- --id name
-
Identifier
- --tags list
-
Add tags
- -h, --help
-
display this help and exit
Vcf parser
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.