Post date: May 13, 2015 4:14:4 PM
The GBS data were aligned to our draft alfalfa genome. First, I indexed the genome:
bwa index -a bwtsw final.assembly.fasta
I then ran the alignments with bwa using a GATK friendly header (here is one example):
cd /pscratch/A01963476/data/gbsGomp006to008/Alignments/
bwa aln -n 5 -l 20 -k 2 -t 8 -q 10 -Y -f alnM-VUH-13-20.sai final.assembly.fasta /pscratch/A01963476/data/gbsGomp006to008/Parsed/M-VUH-13-20.fastq
bwa samse -n 1 -r '@RG\tID:M-VUH-13-20\tPL:ILLUMINA\tLB:M-VUH-13-20\tSM:M-VUH-13-20' -f alnM-VUH-13-20.sam final.assembly.fasta alnM-VUH-13-20.sai /pscratch/A01963476/data/gbsGomp006to008/Parsed/M-VUH-13-20.fastq
The alignments were written to: /pscratch/A01963476/data/gbsGomp006to008/Alignments/. They were then compressed, sorted and indexed with samtools.