VarTools

requests

• python 3.x
• numpy
• pandas
• scipy
• java 1.8 for vardict and GATK
• R(version>=3.6.3) for vardict
• samtools

funcion

1. f2v: analysis from fastq to gvcf.
2. tGT: from gvcf created by GATK to vcf in trio mode.
3. sGT: from gvcf created by GATK to vcf in single mode.
4. cc: case-control analysis with 2 ways.
5. fp: build false positive database for filter.
6. bqc: bam quality check.
7. gd: gender identify.

f2v

python3 VarTools.py f2v -i in_dir -o out_dir -b bed -p prefix --vcf --fastqc --qualimap --keep_tmp -t 6

trio_genotype

python3 VarTools tGT -p .gvcf -f .gvcf -m .gvcf -s .gvcf,.gvcf -o ./result/outName

single_genotype

python3 VarTools sGT -p .gvcf -o ./result/outName

case-control

python3 VarTools cc --case case_dir --control control_dir --mode AD -o result

build false positive databse

python3 VarTools fp -i indir -o ./result --snvdb false_positive.txt --overlap_rate 0.3 --file_type vcf

bam quality check

python3 VarTools bqc -b in.bam --bed bed

gender identify

python VarTools gd -b in.bam -d bed

anno

python VarTools.py anno -i cohort.vcf.gz -o anno_result/ --prefix cohort -t 8 

software

• fastp
• fastqc
• bwa-mem2
• bowtie2
• samtools
  • note: please install by yourself and ensure the ability to execute.
• qualimap
• mosdepth
• sambamba
• plink1.9
• strelka2
• GATK
• bcftools
  • note: please install by yourself and ensure the ability to execute.
• VarDictJava
• htslib
  • note: please install by yourself and ensure the ability of tabix and bgzip to execute.
• SnpEff
• kings
• VariantQC
• annovar
  • note: please download annovar by yourself and move scripts to ./bin/annovar/
• clinSV

database

• GATK
• Reference gap
• SPIDEX 1.0
• omim
• ReVe

some files in lib

• Hg19.genome.bed/Hg38.genome.bed

# Hg38 from GATK
cut -f 1,2 Hg38.fasta.fai | head -n 24 | sort -k1,1  > Hg38.genome
# Hg19 from GATK
cut -f 1,2 Hg19.fasta.fai | sed -n '2,25p' | sort -k1,1  > Hg19.genome
zcat gap.txt.gz | awk -F"\t" '{if ($2~/^.{4,5}$/) print $2"\t"$3"\t"$4 }' | bedtools sort -i stdin > gap.bed
bedtools complement -i gap.bed -g Hg38.genome > Hg38.genome.bed

• VarDict_assembly19_fromBroad_5k_150bpOL_seg.bed

# a bed file for VarDict WGS calling 
bedtools makewindows -g human.hg38.fa.fai -w 50150 -s 50000 > hg38.wgs.bed

some databases built

• ReVe

zcat hg19_ReVe.txt.gz | cut -f 1-5,8 > hg19_ReVe_tmp1.txt
perl index_annovar.pl hg19_ReVe_tmp1.txt -outfile hg19_ReVe.txt -comment comment.txt