Post date: Oct 30, 2019 10:10:18 PM
NOTE: this is where Rozenn began collaborating on the project. We are revisiting alignments and assessing different variant callers. We are beginning by comparing my earlier alignment with bwa aln with bwa mem.
1. Alignment with bwa mem (version 0.7.17-r1188)
From /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/gbs_pando_plus/Parsed
I ran,
perl ../Scripts/wrap_qsub_slurm_bwa_mem.pl *fastq
This submits 2024 alignments, here is one example:
cd /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/gbs_pando_plus/Parsed/
bwa mem -t 8 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:potr-WYW-1650\tPL:ILLUMINA\tLB:potr-WYW-1650\tSM:potr-WYW-1650' /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/genome/Potrs01-genome.fa WYW-1650.fastq > /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/gbs_pando_plus/Alignments_mem/aln_mem_WYW-1650.sam 2> /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/gbs_pando_plus/Alignments_mem/log_mem_WYW-1650.txt
Note, because of the new cap at 1000 jobs, I need to submit these in 3 batches.