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vcf-filter

  • multi-anchors filtering and multi-threads implementation for vcf filtering
    • for each anchor can include several sub-anchors.
    • in singel anchor, pass if all sub-anchors satisfied.

Prerequisite

  • Python 3
  • vcf
    • decomposed & normalized by vt or bcftools
    • annotated by annovar (.vcf, not .txt)

Installation

git clone https://github.com/shanghungshih/vcf-filter.git

Parameters

  • -v --vcfs : the vcfs file which seperate by ','
  • -a --anchors : the information of the counters
  • -t --thread : pool size for multi-thread importing (default: 1)
  • --write2file : to be update

Quick start

  1. without write2file
python3 vcf-filter.py -v sample1.hg19_multianno.vcf,sample2.hg19_multianno.vcf -a anchors/anchors-basic.json -t 2
  1. with write2file
python3 vcf-filter.py -w true -v sample1.hg19_multianno.vcf,sample2.hg19_multianno.vcf -a anchors/anchors-PG-853variant.json

anchors configuration

  1. in anchors, define every anchor name which will show in results.
  2. for each anchor, please define:
    • key: keys presents in info column of annovar-annotated vcf (ex. Func.refGene=TP53;AF=0.001;), and for variant comparison, using variant for key name.
    • type: operator to perform comparison (valid types: ==, >=, <=, >, <, in, not in)
    • value: operand to compare with vcf

Notes

  • count if variant pass all sub-anchors.
  • for input file, only .vcf will be accepted.
  • configure the anchors.json before you run the program, and make sure the key of each sub-anchor appear in your vcf annotation.
  • multi-threads is for multiple vcfs.

example output (using anchors/anchors-basic.json)

  • total: # of total variants
  • pass_anchors: # of variants that pass all sub-anchors in an anchor
INFO     [vcf] : ['sample1.hg19_multianno.vcf', 'sample2.hg19_multianno.vcf']
INFO     [anchors file] : [anchors/anchors-basic.json]
INFO     [anchors] : ['anchors-PASS', 'anchors-AF<0.01', 'anchors-AF<0.05', 'anchors-PASS&AF<0.01', 'anchors-PASS&AF<0.05']
INFO     [write2file] : [False]
INFO     [threads] : [1]
INFO     [anchors-PASS]-[sample1.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [PASS] : 0
INFO
INFO     [anchors-PASS]-[sample2.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [PASS] : 0
INFO
INFO     [anchors-AF<0.01]-[sample1.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [AF<0.01] : 0
INFO
INFO     [anchors-AF<0.01]-[sample2.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [AF<0.01] : 0
INFO
INFO     [anchors-AF<0.05]-[sample1.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [AF<0.05] : 0
INFO
INFO     [anchors-AF<0.05]-[sample2.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [AF<0.05] : 0
INFO
INFO     [anchors-PASS&AF<0.01]-[sample1.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [PASS] : 0
INFO     [AF<0.01] : 0
INFO
INFO     [anchors-PASS&AF<0.01]-[sample2.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [PASS] : 0
INFO     [AF<0.01] : 0
INFO
INFO     [anchors-PASS&AF<0.05]-[sample1.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [PASS] : 0
INFO     [AF<0.05] : 0
INFO
INFO     [anchors-PASS&AF<0.05]-[sample2.hg19_multianno.vcf] (time used: 0.00 min)
INFO     [total] : 20
INFO     [pass_anchors] : 0
INFO     [PASS] : 0
INFO     [AF<0.05] : 0
INFO