Using samtools and Picard tools with cram files

Question

[Chris Gene]

I have a series of cram files that I want to merge without converting to bam. When I try samtools merge out.cram in1.cram in2.cram in3.cram

I get the following error: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). /tmp/1460051111.1957878: line 8: 18355 Segmentation fault

Is there any specification I can add to the merge command to make it work? None of the options seem to do the trick.

Also, can I then pass the cram file to Picard tools BamToFastq?

Thanks

[Devon Ryan]

What version of samtools do you have?

[Devon Ryan]

BTW, there's an --input-fmt-option that you can use.

[Chris Gene]

It's 0.1.18; doesn't work with that option. I'll update and try again. Thanks!

[Devon Ryan]

0.1.18 was written before CRAM was invented...

[GenoMax]

You should upgrade to the latest. That is a fairly old version of samtools.

Answer 1

[Chris Gene]

Worked fine with the update, thanks. And picard's BamToFastq? I'm using v. 1.99, that already supports cram files, but still get parsing error:

Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; Line 1 Line: CRAM^C^@ (...) at net.sf.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:420) at net.sf.samtools.SAMLineParser.parseLine(SAMLineParser.java:210) at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:237) at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:225) at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:201) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:687) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:665) at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:132) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:121)

[John Marshall]

Picard v1.99 is from September 2013, which also pretty much predates the CRAM format and certainly is well before any Picard support for CRAM (which according to ENA was introduced in 1.133, but I too would recommend staying very up-to-date if you want to do anything with CRAM in HTSJDK or Picard).

You might consider samtools fastq for this job.

[Devon Ryan]

I'd suggest using the latest version (2.2.1, I think) of picard as well. Picard's ability to handle CRAM files still seems to be a bit of a work in progress.