bwa from others

Here's what I use for bwa alignment (without removing PCR dups).
You can replace the paths with your own and put into a bash script for automation
comments or corrections welcome!

#Visit kevin-gattaca.blogspot.com to see updates of this template!
#Creates colorspace index
bwa index -a bwtsw -c hg18.fasta
#convert to fastq.gz
perl /opt/bwa-0.5.7/solid2fastq.pl Sample-input-prefix-name Sample
#aln using 4 threads
bwa aln -c -t 4 /data/public/bwa-color-index/hg18.fasta Sample.single.fastq.gz > Sample.bwa.hg18.sai
#for bwa samse
bwa samse /data/public/bwa-color-index/hg18.fasta Sample.bwa.hg18.sai Sample.single.fastq.gz > Sample.bwa.hg18.sam
#creates bam file from pre-generated .fai file
samtools view -bt /data/public/hg18.fasta.fai -o Sample.bwa.hg18.sam.bam Sample.bwa.hg18.sam
#sorts bam file
samtools sort Sample.bwa.hg18.sam.bam{,.sorted}
#From a sorted BAM alignment, raw SNP and indel calls are acquired by:
samtools pileup -vcf /data/public/bowtie-color-index/hg18.fasta Sample.bwa.hg18.sam.bam.sorted.bam > Sample.bwa.hg18.sam.bam.sorted.bam.raw.pileup
#resultant output should be further filtered by:
/opt/samtools/misc/samtools.pl varFilter Sample.bwa.hg18.sam.bam.sorted.bam.raw.pileup | awk '$6>=20' > Sample.bwa.hg18.sam.bam.sorted.bam.raw.pileup.final.pileup