VariantFilter

Optimized for University of Oxford Research Computing HPC. Can be adapted and used on others.

Usage

Example command line usage:

python FilterVariants.py -i AGE_Matched_13Mar2019/mutect2 -a -ref GRCm38.86 -j /users/leedham/rschenck/tools/snpEff/snpEff.jar -t

or ask for help

python FilterVariants.py --help

2020-07-29 10:33:32,239-INFO: Thank you for using Variant Filter. Created by Ryan Schenck...


usage: FilterVariants.py [-h] [-i INDIR] [-c CALLER] [-ievs] [-nr MINNR]
                         [-vr MINVR] [-vd VARSAMDEPTH] [-af MINVAF]
                         [-e MAXEVENTS] [-l CLUSTERFLANK] [-t] [-u]
                         [--samplemap SAMPLEMAP] [-uvr UMINVR] [-uaf UMINVAF]
                         [-v] [-a] [-ref REF] [-j JARFILE]
                         [-reffasta REFGENOME]

optional arguments:
  -h, --help            show this help message and exit
  -i INDIR              Input directory of vcf files with .passed.vcf
                        extension, in the case of Strelka2 it expects the
                        directory containing all information. Default: ./
  -c CALLER             Callers to be used, 1) MuTect2 2) Strelka2 3) Octopus
                        4) Shearwater ML; Default: 1) MuTect2
  -ievs                 Whether to ignore the LowEVS filter on Strelka2
                        output. Default=False. (Only applies for Strelka2
                        caller)
  -nr MINNR             Minimum reads in normal. Default: 10
  -vr MINVR             Minimum variant reads. Default: 2
  -vd VARSAMDEPTH       Total reads at variant site sum(ref,alt). Default=10
  -af MINVAF            Minimum variant allele frequency. Default=0.1
  -e MAXEVENTS          Maximum number of events allowed at a loci. This
                        ignores germline for example. Default=1
  -l CLUSTERFLANK       Flanking region to omit clustered events. Default: 10
  -t                    Flag to build an informative table. Useful for quick R
                        processing without additional Bioconductor packages.
  -u, --usesamplemap    Boolean indicating whether to use same sample filter
                        options. Default: True, must specify --samplemap
                        <file>.
  --samplemap SAMPLEMAP
                        File with sample mapping in comma separated text file.
                        Default: None, required if -u
  -uvr UMINVR           Minimum variant reads if -u setting is present.
                        Default: 2
  -uaf UMINVAF          Minimum variant allele frequency if -u setting is
                        present. Default: 0.005
  -v                    Verbosity setting. Use -v to suppress some stdout.
  -a                    Annotate using snpEff. This requires -ref and -j.
                        Default=F
  -ref REF              Reference genome to be used for snpEff annotations
                        (See http://snpeff.sourceforge.net/index.html).
                        Default=None
  -j JARFILE            snpEff.jar executable (See
                        http://snpeff.sourceforge.net/index.html) Default=None
  -reffasta REFGENOME   Reference genome that the variants are called with. De
                        fault=/well/leedham/users/rschenck/References/Ensembl/
                        GRCm38/Mus_musculus.GRCm38.dna.primary_assembly.fa