This repository contains set of slurm scripts used for processing and analysing short read whole genome sequencing dataset. The germline analysis performed using DeepVariant v1.5.0 on the "normal" sample whereas the somatic snvs/indels are called using VarScan2.4.6 Please modify it accordingly based on the environment
Resource allocation and account info in each slurm script needs to be modifed
Step 1. Trimming with fastp 1_fastp_array.sl
Step 2. Aligning against reference genome with BWA 2_bwa_array.sl
Step 3. Create list of files each containing path to bam multple files that belong to one sample 3_makeBamList.sh
Step 4. Merge bam files based on files created in Step 3. 4_merge_bam_array.sl
Step 5. Sort bams by genomic coordinates 5_sortbam_array.sl
Step 6. Remove/mark PCR duplicated using Piacrd Tools 6_rmduplicates_array.sl
Step 7. Collect useful metrics using Picard Tools 7_CollectWgsMetrics_array.sl
Step 8. Run Google DeepVariant 8_run_dv.sl
Step 9. Submit VarScan2 somatic analysis on each chromosome seperately since VarScan2 itself is not parallelized 9_submit_per_chr_varscan2_job.sh