vcf-contrast (1)

vcf-contrast +<list> -<list> [OPTIONS] file.vcf.gz

About: Finds differences amongst samples adding NOVEL* annotation to INFO field.

+<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