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CRAM is reference based compression so may or may not be of interest for you. http://www.ebi.ac.uk/ena/about/cram_toolkit/
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Hi all, I can't figure out how to specify loseless compression using cramTools (ie retain all quality score info), can someone help me out? In NGCs paper they state a few flags which seem to be discontinued in 1.0. Presumably I specify using --lossy-quality-score-spec but I can't figure out how to set it to 'any/all'. I appreciate any help/ideas on this. Also if I am missing the point and the compression inherently removes quality scores I apologise in advance, I am n00 to the area=PLast edited by bruce01; 01-11-2013, 02:55 AM.
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Hi,
I'm in the same situation as Bruce. I want to compress keeping the base call qualities but can't figure out how...
Just did a naïf try:Code:--lossy-quality-score-spec all
Code:Exception in thread "main" java.lang.RuntimeException: Uknown read or base category: a at net.sf.cram.lossy.QualityScorePreservation.parseSinglePolicy(QualityScorePreservation.java:138)
Thanks!
Pablo.
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Hi Pablo,
found it on the archives of cram mailing list, the call includes: -L m999 (-L flag is your --lossy-quality-score-spec above). All reads are retained, but you lose column 12+ ('info'). This isn't an issue for me, and the compressed cram file for a 1GB bam is 600MB which is pretty good!
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I just noticed this thread, rather late.
There is CRAM from EBI, which has long term support and handles random access. It's the most direct competitor to BAM I would guess.
Alternatives are Goby (similar ratios, but even slower from my experience), Quip (faster encoding, great compression ratio, but no(?) random access) and SamComp1/2 (faster encoding, great compression ratio, no random access, and doesn't really implement the full SAM spec - more of a fastq compressor). Finally on that topic there are tools like quip again, fqzcomp and fastqz for compression of FASTQ data. [All 3 of these were SequenceSqueeze competition entries.]
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But as I saw in one of the presentations, it seems CRAM does a lossy conversion from BAM, and introduces false positive and false negatives ? Is CRAM mature now to do a lossless compression from FASTQ and BAM files with random access such as BAM files give ?
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