Post date: Jan 23, 2015 4:51:25 PM
I concatenated the available C. maculatus genome sequence and the final GBS contigs, and then indexed the genome with bwa:
bwa index -a bwtsw cmacbbg9jan14gbs.fasta
I used bwa aln and samse to align the sequence data for each of the 576 seed beetles the reference genome. Note, the options are mostly what I have been using but I increased the maximum number of missmatches to 5 and removed casava filtered reads (-Y). I submitted the jobs with perl ../../Scripts/wrap_qsub_rc_bwa.pl /labs/evolution/data/callosobruchus/gbs/Parsed/[LM]*fastq. Here is an example command:
cd /labs/evolution/data/callosobruchus/gbs/Assemblies/gbs2ref/
bwa aln -n 5 -l 20 -k 2 -t 8 -q 10 -Y -f alnM-14-48.sai cmacbbg9jan14gbs.fasta /labs/evolution/data/callosobruchus/gbs/Parsed/M-14-48.fastq
bwa samse -n 1 -r '@RG ID:cmac-M-14-48' -f alnM-14-48.sam cmacbbg9jan14gbs.fasta alnM-14-48.sai /labs/evolution/data/callosobruchus/gbs/Parsed/M-14-48.fastq