alignment of GBS for ancestry inference to melissa genome

Post date: Apr 28, 2016 9:9:18 PM

My plan is to align previous GBS data to the L. melissa genome and use these data to infer ancestry blocks. To this end, I am aligning all of the 'alpine' and 'warners' samples we have, as well as putative parents, L. anna, L. ricei, L. idas, and L. meliss. For L. idas and L. melissa I am using a subset of samples. For alpine, I want L. anna and L. melissa (BHP, GVL, REW, SLA, VCP, and WAL), and for warners I want L. anna or L. ricei or L. idas, with the aforementioned L. melissa, or more likely, DCR, GLA, LAC, OCY, SSC, and SUV (based on geography and results from the 2014 admixture paper).

Alignments will be here: /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_gbs/AssembliesHybAncestry

hyancbams is a list of relevant bam files, it contains 41 populations and 922 individuals, per population sample sizes are below.

I used bwa () for the alignments, specifically the samese and aln algorithms (bwa 0.7.10-r789). Here is an example command for one individual:

cd /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_gbs/AssembliesHybAncestry

bwa aln -n 4 -l 20 -k 2 -t 8 -q 10 -f alnYBG12-99M.sai /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/melissa_genome/final.assembly.fasta YBG12-99M.fastq

bwa samse -n 1 -r '@RG\tID:lyc-YBG12-99M\tPL:ILLUMINA\tLB:lyc-YBG12-99M\tSM:lyc-YBG12-99M' -f alnYBG12-99M.sam /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/melissa_genome/final.assembly.fasta alnYBG12-99M.sai YBG12-99M.fastq

Sorting, compressing, and indexing alignment with samtools (version 1.2), here is an example command:

cd /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_gbs/AssembliesHybAncestry/

samtools view -b -S -o alnYBG12-99M.bam alnYBG12-99M.sam

samtools sort alnYBG12-99M.bam alnYBG12-99M.sorted

samtools index alnYBG12-99M.sorted.bam