Post date: Mar 24, 2016 3:25:39 AM
I used bwa (version 0.7.10-r789) aln and samse to align the Fallon data to our alfalfa reference genome.
cd /uufs/chpc.utah.edu/common/home/gompert-group1/data/alfalfa/gbs/fallon/Parsed/
bwa aln -n 5 -l 20 -k 2 -t 8 -q 10 -f alnfal50.sai /uufs/chpc.utah.edu/common/home/gompert-group1/data/alfalfa/genome/Msativa/DATA/RUN/ASSEMBLIES/assem1feb15/final.assembly.fasta fal50.fastq
bwa samse -n 1 -r '@RG\tID:fal-fal50\tPL:ILLUMINA\tLB:fal-fal50\tSM:fal-fal50' -f alnfal50.sam /uufs/chpc.utah.edu/common/home/gompert-group1/data/alfalfa/genome/Msativa/DATA/RUN/ASSEMBLIES/assem1feb15/final.assembly.fasta alnfal50.sai fal50.fastq
I then used samtools (1.2) to compress, sort, and index the alignment (in the Alignments subdirecory), here is an example:
cd /uufs/chpc.utah.edu/common/home/gompert-group1/data/alfalfa/gbs/fallon/Alignments/
samtools view -b -S -o alnfal50.bam alnfal50.sam
samtools sort alnfal50.bam alnfal50.sorted
samtools index alnfal50.sorted.bam