Converting multiple cram files to fastq files.
1 answer
using a Makefile
BAMS=$(shell find /path/to/dir -type f -name "*.cram" )
FASTQS=$(addsuffix .R1.fastq.gz,$(basename $(BAMS)))
REF=/path/to/ref.fa
%.R1.fastq.gz: %.cram
samtools collate --reference $(REF) -O -u -f --no-PG $< |\
samtools bam2fq -1 $@ -2 $(addsuffix .R2.fastq.gz,$(basename $<))
all: $(FASTQS)
invoke with make -j <number-of-threads>
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Pierre Lindenbaum
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