This is the command vcf_filter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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)
Use vcf_filter online using onworks.net services
