Converting Bam To Fastq

Question

[Zach Stednick]

Any suggestions on good programs or scripts to convert a BAM file back to a fastq? I have found some scripts but wanted to ask for advice before I go too far down the wrong path.

[Mike Muratet]

Do you know the rules for identifying mate pairs? I used bowtie to align some paired end reads into a sam format file and was able to use various picard methods to process it. I made a file with duplicates removed and SamToFastq throws an exception:

Exception in thread "main" net.sf.picard.PicardException: Illegal mate state: HWUSI-EAS614_1:1:12:4379:1523:0:2:1
at net.sf.picard.sam.SamToFastq.assertPairedMates(SamToFastq.java:231)
at net.sf.picard.sam.SamToFastq.doPaired(SamToFastq.java:140)
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:95)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:87)

I assume because the read ID is not HWUSI-EAS614_1:1:12:4379:1523/2

Have you any had any problems like this?

Thanks

Mike

[Zach Stednick]

I have not. Maybe you should ask this as an independent question to have more people view and potentially offer assistance.

[Teja]

Mike, Did you find a way around it? Im facing the same problem.

Thanks, Teja

[Khader Shameer]

Teja, please ask your problem as a separate question for detailed response.

Answer 1

[Pierre Lindenbaum]

Use SamToFastq

UPDATE 2023: use samtools collate piped into samtools fastq

[bshifaw]

You can use Picard

java -jar picard.jar SamToFastq \
     I=input.bam \
     FASTQ=output.fastq

http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq

[Ram]

I moved this comment here as it's adds to Pierre's answer and is not a unique answer of its own.

[Pierre Lindenbaum]

hu ? I wonder why someone flagged this as negative ???!! :-/

Answer 2

[Casey Bergman]

There is a bam2fastx utility bundled with tophat:

bam2fastx [--fasta|-a|--fastq|-q] <in.bam>

[Adrian Pelin]

Works really really well for me:

bam2fastx --fastq -M -o S1_mapped.fastq -N S1.sort.grp.md.bam

Here it adds the /1 and /2 suffix for paired reads and doesn't complain if mate is missing (some of my reads are single ended and don't have a mate). Bam2Fastq would complain about missing mates and wouldn't export single ended reads unless extra precautions were taken.

Answer 3

[Aaronquinlan]

There is also one in the Hydra package. It's called bamToFastq.

Answer 4

[Doctoroots]

Here is another tool that saves the transition into sam format and converts bam directly into fastq: bam2fastq

[Charles Plessy]

By the way, the URL changed to https://gsl.hudsonalpha.org/information/software/bam2fastq, but the software is deprecated in favour of Picard.

Answer 5

[Ron]

Bedtools - for converting bam to fastq http://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html