Whole Exome Squence Snakemake

Germline Single-Sample Pipeline

Conda Enviornment

conda install -c bioconda -c conda-forge bowtie sra-tools samtools bcftools vcftools snpeff fastp bowtie2 bwa bowtie bedtools snakemake

GATK Download

wget  https://github.com/broadinstitute/gatk/releases/download/4.0.6.0/gatk-4.0.6.0.zip
unzip gatk-4.0.6.0.zip
cd gatk-4.0.6.0
./gatk --help

Files needed for analysis

Homo_sapiens_assembly38

wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz  
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.fai  
unzip Homo_sapiens_assembly38.fasta.gz

dbsnp

wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/dbsnp_146.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/dbsnp_146.hg38.vcf.gz.tbi

indels

wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz 
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi

How To Execute

Germline:

snakemake -s WES_snakemake.py -p -j 1 --config workspace=path-to-workspace \
genomes=path-to-bwa-index GATK=path-to-gatk \
ref=path-to-Homo_sapiens_assembly38.fasta \
snp=path-to-dbsnp_146.hg38.vcf.gz \
indel=path-to-path-to-Mills_and_1000G_gold_standard.indels.hg38.vcf.gz

Somatic:

snakemake -s somatic_SNV_Indel.snakemake \
--configfile somatic_SNV_Indel.yaml -j 12 -p

This pipeline is in the process of being updated.......