This is the command vcf-subset 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-subset - create subset of VCF file
SYNOPSIS
vcf-subset [OPTIONS] in.vcf.gz > out.vcf
OPTIONS
-c, --columns <string>
File or comma-separated list of columns to keep in the vcf file. If file, one
column per row
-e, --exclude-ref
Exclude rows not containing variants.
-p, --private
Print only rows where only the subset columns carry an alternate allele.
-r, --replace-with-ref
Replace the excluded types with reference allele instead of dot.
-t, --type <list>
Comma-separated list of variant types to include: SNPs,indels.
-u, --keep-uncalled
Do not exclude rows without calls.
-h, -?, --help
This help message.
EXAMPLES
cat in.vcf | vcf-subset -r -t indels -e -c SAMPLE1 > out.vcf
Use vcf-subset online using onworks.net services
