NGS crash course

Makefile

#http://samtools.sourceforge.net/mpileup.shtml

SAMDIR=/usr/local/package/samtools-0.1.18
SAMTOOLS=$(SAMDIR)/samtools
BCFTOOLS=$(SAMDIR)/bcftools/bcftools
BWA=/usr/local/package/bwa-0.6.1/bwa
REF=chr22.fa

.INTERMEDIATE : align.sam random_1.sai random_2.sai align.bam variations.bcf

%.bam : %.sam
	$(SAMTOOLS) view -o $@ -b -S -T $(REF) $<
%.bam.bai : %.bam
	$(SAMTOOLS) index $<


variations.vcf: variations.bcf
	$(BCFTOOLS) view $< > $@

variations.bcf : align.sorted.bam align.sorted.bam.bai
	    $(SAMTOOLS) mpileup -uf $(REF) $< | $(BCFTOOLS) view -bvcg - > $@

align.sorted.bam : align.bam
	$(SAMTOOLS) sort $< align.sorted


align.sam : random_1.sai random_2.sai  
	$(BWA) sampe $(REF) $^ random_1.fq.gz random_2.fq.gz > $@

$(REF):
	curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/$(REF).gz" |\
	gunzip -c | grep -v N | head -n 100000 > $@


random_1.sai :  random_1.fq.gz $(REF).bwt
	$(BWA) aln -f $@ $(REF) $<

random_2.sai :  random_2.fq.gz $(REF).bwt
	$(BWA) aln -f $@ $(REF) $<

random_1.fq.gz random_2.fq.gz : $(REF)
	$(SAMDIR)/misc/wgsim -N 1000000 $< random_1.fq random_2.fq > wgsim.output
	gzip -f --best random_1.fq random_2.fq

$(REF).bwt : $(REF)
	$(BWA) index -a bwtsw $<

$(REF).fai :  $(REF)
	$(SAMTOOLS) faidx $< 



clean:
	rm -f chr22.* *.bam *.vcf *.bcf *.sai *.gz *.fq *.bai  wgsim.output *.sam