makefiles/bsqr.mk

   1 BAMS = $(sort $(wildcard *.bam))
   2 BAMF = $(patsubst %.bam,%,$(BAMS))
   3 OUT1 = $(addsuffix .recal.tbl,$(BAMF))
   4 OUT3 = $(addsuffix .post.tbl,$(BAMF))
   5 OUT4 = $(addsuffix .cmp.pdf,$(BAMF))
   6 OUT2 = $(addsuffix .recalbam,$(BAMF))
   7
   8 REF := /bak/seqdata/genomes/Felis_catus_80_masked/Felis_catus80_chr.fa
   9
  10 .PHONY: all
  11
  12 all: $(OUT1) $(OUT2) $(OUT3) $(OUT4)
  13         echo [$(BAMS)] -> [$(OUT2)]
  14
  15 %.recal.tbl: %.bam
  16         gatk -T BaseRecalibrator -nct 8 -mte -R $(REF) -I $(*).bam -knownSites filtered2.vcf -o $@ 2>$@.log
  17
  18 %.post.tbl: %.recal.tbl %.bam
  19         gatk -T BaseRecalibrator -nct 8 -mte -R $(REF) -I $(*).bam -knownSites filtered2.vcf -BQSR $(@:.post.tbl=.recal.tbl) -o $@ 2>$@.log
  20
  21 %.cmp.pdf: %.recal.tbl %.post.tbl
  22         gatk -T AnalyzeCovariates -R $(REF) -before $(@:.cmp.pdf=.recal.tbl) -after $(@:.cmp.pdf=.post.tbl) -plots $@ 2>$@.log
  23
  24 %.recalbam: %.recal.tbl %.bam
  25         gatk -T PrintReads -R $(REF) -I $(*).bam -BQSR $(@:.recalbam=.recal.tbl) -o $@ 2>$@.log