Provided by: pyvcf_0.6.8+git20170215.476169c-1build1_all
vcf_filter - 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: 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)