table of contents
| VCF-CONTRAST(1) | User Commands | VCF-CONTRAST(1) |
NAME¶
vcf-contrast - finds differences amongst samples
SYNOPSIS¶
vcf-contrast +<list> -<list> [OPTIONS] file.vcf.gz
DESCRIPTION¶
About: Finds differences amongst samples adding NOVEL* annotation to INFO field.
OPTIONS¶
- +<list>
- List of samples where unique variant is expected
- -<list>
- List of background samples
- -d, --min-DP <int>
- Minimum depth across all -<list> samples
- -f, --apply-filters
- Skip sites with FILTER column different from PASS or "."
- -n, --novel-sites
- Print only records with novel genotypes
- -h, -?, --help
- This help message.
Example:¶
- # Test if any of the samples A,B is different from all C,D,E vcf-contrast +A,B -C,D,E -m file.vcf.gz
- # Same as above but printing only sites with novel variants and table output vcf-contrast -n +A,B -C,D,E -m file.vcf.gz | vcf-query -f '%CHROM %POS\t%INFO/NOVELTY\t%INFO/NOVELAL\t%INFO/NOVELGT[\t%SAMPLE %GTR %PL]\n'
- # Similar to above but require minimum mapping quality of 20 vcf-annotate -f MinMQ=20 file.vcf.gz | vcf-contrast +A,B,C -D,E,F -f
| February 2013 | vcf-contrast |