.TH VCF_FILTER "1" "October 2015" "0.6.7" "User Commands"
.SH NAME
vcf_filter \- Filter a VCF file
.SH SYNOPSIS
.B vcf_filter
[\-h] [\-\-no\-short\-circuit] [\-\-no\-filtered]
[\-\-output OUTPUT] [\-\-local\-script LOCAL_SCRIPT]
input filter [filter_args] [filter [filter_args]] ...
.SH DESCRIPTION
This script is part of PyVCF.
.SH OPTIONS
.SS "positional arguments:"
.TP
input
File to process (use \- for STDIN) (default: None)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit. (default: False)
.TP
\fB\-\-no\-short\-circuit\fR
Do not stop filter processing on a site if any filter
is triggered (default: False)
.TP
\fB\-\-output\fR OUTPUT
Filename to output [STDOUT] (default:
<_io.TextIOWrapper name='<stdout>' mode='w'
encoding='ANSI_X3.4\-1968'>)
.TP
\fB\-\-no\-filtered\fR
Output only sites passing the filters (default: False)
.TP
\fB\-\-local\-script\fR LOCAL_SCRIPT
Python file in current working directory with the
filter classes (default: None)
.SS "mgq:"
.IP
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.
.TP
\fB\-\-genotype\-quality\fR GENOTYPE_QUALITY
Filter sites with no genotypes above this quality
(default: 50)
.SS "snp-only:"
.IP
Choose only SNP variants
.SS "dps:"
.IP
Threshold read depth per sample
.TP
\fB\-\-depth\-per\-sample\fR DEPTH_PER_SAMPLE
Minimum required coverage in each sample (default: 5)
.SS "avg-dps:"
.IP
Threshold average read depth per sample (read_depth / sample_count)
.TP
\fB\-\-avg\-depth\-per\-sample\fR AVG_DEPTH_PER_SAMPLE
Minimum required average coverage per sample (default:
3)
.SS "eb:"
.IP
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
.TP
\fB\-\-eblr\fR EBLR
Filter sites above this error log odds ratio (default:
\fB\-10\fR)
.SS "sq:"
.IP
Filter low quailty sites
.TP
\fB\-\-site\-quality\fR SITE_QUALITY
Filter sites below this quality (default: 30)