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)