---
name: "vcf-contrast"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf-contrast"
---

# vcf-contrast(1)

finds differences amongst samples

## 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**

-