vcf-contrast(1) finds differences amongst samples


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


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


List of samples where unique variant is expected
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.


# 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