vcf_filter(1) Filter a VCF file


vcf_filter [-h] [--no-short-circuit] [--no-filtered] [--output OUTPUT] [--local-script LOCAL_SCRIPT] input filter [filter_args] [filter [filter_args]] ...


This script is part of PyVCF.


positional arguments:

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

optional arguments:

-h, --help
Show this help message and exit. (default: False)
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'>)
Output only sites passing the filters (default: False)
--local-script LOCAL_SCRIPT
Python file in current working directory with the filter classes (default: None)


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)


Choose only SNP variants


Threshold read depth per sample
--depth-per-sample DEPTH_PER_SAMPLE
Minimum required coverage in each sample (default: 5)


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)


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)


Filter low quailty sites
--site-quality SITE_QUALITY
Filter sites below this quality (default: 30)