grep_vcf is a tiny tool to filter vcf file based on position file and vice et versa.
grep_vcf - filter vcf to keep lines that match positions given in reference file.
positional arguments:
positions The text file with the positions looking for in vcf file. It
must be a tsv file (https://en.wikipedia.org/wiki/Tab-separated_values).
Where position are in first column.
Lines starting with '#' are considering as comments.
optional arguments:
-h, --help show this help message and exit
--vcf VCF The path to the vcf file. By default grep_vcf search for the
same path as position file but with '.vcf' as extension.
--out OUT The path to an output file, default is stdout. If the file
exists, it will be replaced.
--invert, -v Invert the sense of matching, to select non-matching vcf
lines.
--switch Filter position file to keep lines that position match in vcf
--version, -V Display version information and quit.
pip install git@https://github.com/bneron/grep_vcf.git#egg=grep_vcfgrep_vcf is developed and released under open source licence GPLv3
We encourage contributions, bug report, enhancement ...
But before to do that, we encourage to read the contributing guide.