vcf-contrast - finds differences amongst samples
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.
- # 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