vcf-contrast1
Finds differences amongst samples
Usage
vcf-contrast +<list>
-<list>
[OPTIONS]
file.vcf.gz
Overview
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-mfile.vcf.gz
-
# Same as above but printing only sites with novel variants and table output vcf-contrast
-n+A,B-C,D,E-mfile.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
-fMinMQ=20 file.vcf.gz | vcf-contrast +A,B,C-D,E,F-f
Releases
Unchanged in 6 releases since Debian 8 (Jessie).