VariantsQC

A use friendly tool for single sample variants quality control with vcf format. Note: This tool is only for VCF file generate by GATK 4.x.

request

• please add ANNOVAR script to bin directory include:annotate_variation.pl, coding_change.pl, convert2annovar.pl, table_annovar.pl
• python3.x
• python package: pandas，feather-format, numpy ,tenserflow 2.x, tqdm
• samtools (set samtools as executable command)

quickly start

0. Separating multi-allelic variants

bcftools norm -m -any -f Homo_sapiens_assembly38.fasta raw.vcf.gz -Oz --threads 6 > raw.norm.vcf.gz

• There are several ways to do this. We use Bcftools to accomplish these step.
• Please note that if you do not properly separate out multi-allelic variants, VariantsQC will automatically remove that variant in later steps.

1. get annotated matrix

python 1_vcf2matrix.py -i raw.norm.vcf.gz -o annoWithSeq.matrix.tsv -r Homo_sapiens_assembly38.fasta -d /Path_of_humandb/ --thread 6 -j 32 --reserved

• There are several parameters you can find by python 1_vcf2matrix.py -h
  • -i, --vcf: you must have a variants file generate by GATK with vcf format.
  • -o, ---annofile: you can set result name or generated named result.matrix.
  • -r, --reference: the chromosome in the reference must start with chr or you change the script getRef.sh in bin: remove chr in line 8.
  • -d, --humandb: database of annovar, and have: hgxx_refGene, hgxx_rmsk, hgxx_cpgIslandExt, hgxx_genomicSuperDups
  • -t, --tmp: temp directory, [./tmp/]
  • --dp: depth for filter variants. [0]
  • --refTag: reference of variants hg19/hg38. [hg38]
  • --thread: thread of annovar annotation. [1]
  • -j, --job: multiple running to get reference, if set -j > 1, please install parallel. [1]
  • -n, --paranum: number of lines that get reference one job, please set -j > 1. Recommend 50k-1m. [100000]
  • --reserved: Whether to reserved temp documents.

2. filter with multi dnn