finds differences amongst samples
+<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