bio-vcf - domain specific language (DSL) for processing the VCF
format
bio-vcf [options] filename
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
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.