WES

A Whole Exome Sequencing (WES) analysis workflow

Quick start

Set up tools

Follow above link to install and set up all related tools.

Alignment

nohup bash $WES/alignment.sh ../genome mm10 fastq-2 align_mouse 5 &> align_mouse.out

nohup bash $WES/alignment.sh ../genome mm10 fastq-2 align_mouse 5 &> align_mouse.out

Xenofilter [optional]

nohup Rscript $WES/xenofilter.R "align_human" "*.hg38" "align_mouse" "*.mm10" 30 &> xenofilter.out & 

mv Filtered_bams/XenofilteR.log xenofilter.log

mkdir align_xenofilter
for f in Filtered_bams/*; 
	do b=`basename $f`; o=${b/_Filtered.bam/.xenofilter.bam}; 
	mv -v $f align_xenofilter/$o; 
done

rm -rv Filtered_bams/

Run GATK pipeline

nohup bash $WES/run_pipeline.sh ../genome hg38 bam "*" > run_pipeline.out

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This pipeline developed by Sonakshi Bhalla (bhallasonakshi@gmail.com) and Abolfazl Arab (abarbiology@gmail.com) at Goodarzi Lab, UCSF – 2021-2022.