NGS training @GIS

PATH=/usr/local/samtools:/usr/local/samtools/bcftools:/mnt/software/mappers/bwa:$PATH

put files to ~/refgenome/reference.fa ~/prj1/reads.fastq

#1. index step
cd ~/refgenome
bwa index -a is reference.fa
samtools faidx ./reference.fa

#2. align and pileup
cd ~/prj1
bwa aln ../refgenome/reference.fa ./reads.fastq >reads.bwa.aln.sai
bwa samse ../refgenome/reference.fa ./reads.bwa.aln.sai reads.fastq >reads.bwa.aln.sam
samtools import ../refgenome/reference.fa.fai ./reads.bwa.aln.sam reads.bwa.aln.bam
samtools sort reads.bwa.aln.bam reads.bwa.aln.sorted
samtools index reads.bwa.aln.sorted.bam
samtools mpileup -f ../refgenome/reference.fa reads.bwa.aln.sorted.bam >temp.pileup
samtools mpileup -ugf ../refgenome/reference.fa reads.bwa.aln.sorted.bam >reads.bwa.aln.sorted.pileup

#3. call variant file
bcftools view -bcvg reads.bwa.aln.sorted.pileup >var.row.bcf
bcftools view var.row.bcf |vcfutils.pl varFilter -D 100 >var.filt.vcf
more var.filt.vcf

#4. download and install tablet
http://bioinf.scri.ac.uk/tablet/download.shtml
use tablet to view reads.bwa.aln.sorted.bam