Makefile for running lumpy-sv

Makefile

.SECONDARY:

LUMPY:=./lumpy-sv
YAHADB:=./refs/hg19.X11_01_65525S
YAHA:=./yaha
BWA:=./bwa-0.6.2/bin/bwa
BWADB:=./refs/hg19.fa
READ_LENGTH=100

%.um.fq : %.bam
	samtools view $< | $(LUMPY)/scripts/split_unmapped_to_fasta.pl -b 20 > $@

%.yaha.sr.bam : %.um.fq
	$(YAHA) -x $(YAHADB) -q $< -osh stdout -M 15 -H 2000 -L 11 | samtools view -Sb - > $@

%.sr.bam : %.um.fq
	$(BWA) bwasw -H $(BWADB) $< | samtools view -Sb - > $@

%.pe.histo : %.bam
	samtools view $< | $(LUMPY)/scripts/pairend_distro.pl -rl $(READ_LENGTH) -X 4 -N 10000 -o $@

%.sr.bedpe : %.sr.bam
	$(LUMPY)/bin/lumpy -mw 4 -tt 1e-3 -sr bam_file:$<,back_distance:20,weight:1,id:1,min_mapping_threshold:1 > $@

##########
# FIXME-- 
# The steps below will not work correctly without properly specifying the insert size mean and stdev
##########

%.pe.bedpe : %.pe.bam %.pe.histo
	$(LUMPY)/bin/lumpy -mw 4 -tt 1e-3 -pe bam_file:$*.pe.bam,histo_file:$*.pe.histo,mean:500,stdev:50,read_length:$(READ_LENGTH),min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1 > $@

%.pesr.bedpe : %.pe.bam %.sr.bam %.pe.histo
	$(LUMPY)/bin/lumpy -mw 4 -tt 1e-3 -pe bam_file:$*.pe.bam,histo_file:$*.pe.histo,mean:500,stdev:50,read_length:$(READ_LENGTH),min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1 -sr bam_file:$*.sr.bam,back_distance:20,weight:1,id:1,min_mapping_threshold:1 > $@