Converting multiple cram files to fastq files.

Question

[Rose]

Hello everyone, I need help with converting cram files to fastq files. I have many cram files with me and want to convert them to fastq files at once. I am using samtools for conversion. Is there any possible way to do that ??

[GenoMax]

You can simply use a for loop to go through all files or submit parallel jobs if you are on a cluster and can use a job scheduler.

[Rose]

Can you please give the code with for loop, I am actually new to scripting and tried a lot but none of them working.

[Ram]

Do not delete posts that have received feedback. Show us something that you've tried and tell us how it failed.

Answer 1

[Pierre Lindenbaum]

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>