---
name: "vcf_filter"
section: "1"
platform: "linux"
package: "pyvcf"
version: "0.6.8+git20170215.476169c-11"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf_filter"
---

# vcf\_filter(1)

Filter a VCF file

## NAME

vcf\_filter - Filter a VCF file

## SYNOPSIS

**vcf\_filter** \[-h\] \[--no-short-circuit\] \[--no-filtered\] \[--output OUTPUT\] \[--local-script LOCAL\_SCRIPT\] input filter \[filter\_args\] \[filter \[filter\_args\]\] ...

## DESCRIPTION

This script is part of PyVCF.

## OPTIONS

### positional arguments:

- input

  File to process (use - for STDIN) (default: None)

### optional arguments:

- **-h**, **--help**

  Show this help message and exit. (default: False)

- **--no-short-circuit**

  Do not stop filter processing on a site if any filter is triggered (default: False)

- **--output** OUTPUT

  Filename to output \[STDOUT\] (default: \<\_io.TextIOWrapper name='\<stdout\>' mode='w' encoding='ANSI\_X3.4-1968'\>)

- **--no-filtered**

  Output only sites passing the filters (default: False)

- **--local-script** LOCAL\_SCRIPT

  Python file in current working directory with the filter classes (default: None)

### mgq:

-

  Filters sites with only low quality variants. It is possible to have a high site quality with many low quality calls. This filter demands at least one call be above a threshold quality.

- **--genotype-quality** GENOTYPE\_QUALITY

  Filter sites with no genotypes above this quality (default: 50)

### snp-only:

-

  Choose only SNP variants

### dps:

-

  Threshold read depth per sample

- **--depth-per-sample** DEPTH\_PER\_SAMPLE

  Minimum required coverage in each sample (default: 5)

### avg-dps:

-

  Threshold average read depth per sample (read\_depth / sample\_count)

- **--avg-depth-per-sample** AVG\_DEPTH\_PER\_SAMPLE

  Minimum required average coverage per sample (default: 3)

### eb:

-

  Filter sites that look like correlated sequencing errors. Some sequencing technologies, notably pyrosequencing, produce mutation hotspots where there is a constant level of noise, producing some reference and some heterozygote calls. This filter computes a Bayes Factor for each site by comparing the binomial likelihood of the observed allelic depths under: \* A model with constant error equal to the MAF. \* A model where each sample is the ploidy reported by the caller. The test value is the log of the bayes factor. Higher values are more likely to be errors. Note: this filter requires rpy2

- **--eblr** EBLR

  Filter sites above this error log odds ratio (default: **-10**)

### sq:

-

  Filter low quailty sites

- **--site-quality** SITE\_QUALITY

  Filter sites below this quality (default: 30)