makefiles/indel.mk

   1 BAMS = $(sort $(wildcard *.recal.bam))
   2 BAMF = $(patsubst %.recal.bam,%,$(BAMS))
   3 OUT1 = $(addsuffix .realignbam,$(BAMF))
   4
   5 REF := /bak/seqdata/genomes/Felis_catus_80_masked/Felis_catus80_chr.fa
   6
   7 .PHONY: all
   8
   9 all: $(OUT1)
  10         echo [$(BAMS)] -> [$(OUT1)]
  11
  12 %.realignbam: %.recal.bam
  13         gatk -T IndelRealigner -LOD 1 -model USE_READS -R $(REF) -I $(*).recal.bam -targetIntervals indelzones.intervals -o  $@ 2>$@.log
  14
  15 # gatk -T RealignerTargetCreator -R ../ref/Felis_catus80_chr.fa -I bam0.list -o indelzones.intervals -nt 24 -et STDOUT -K /opt/jar/huxs_pku.edu.cn.key -log indelzones.log &