xenial (1) vcf_filter.1.gz

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)