This is the command vcf-contrast that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use vcf-contrast online using onworks.net services
