Question: Is samtools' compression of bam to cram lossless?
gravatar for bjarki.sigurjons
3 days ago by
bjarki.sigurjons10 wrote:

One can use CRAMtools to convert(compress) bam into cram. CRAMtools has options to allow for lossy and non-lossy compression (--lossless-quality-score and --lossy-quality-score-spec).

Samtools is also capable of compressing bam into CRAM but with limited parameteres, one just specifies the output to be cram (using option -C). So my question is, do you know if the samtools' compression of bam into cram is lossy or lossless?


cram samtools • 101 views
ADD COMMENTlink modified 3 days ago by Devon Ryan64k • written 3 days ago by bjarki.sigurjons10

My guess is that it will be 'lossless'. If it were lossy, it must have been documented. You can easily check it by yourself. Get a sam -> convert to bam -> cram -> sam. Then compare this sam with original sam.

ADD REPLYlink written 3 days ago by Santosh Anand1.5k
gravatar for Devon Ryan
3 days ago by
Devon Ryan64k
Freiburg, Germany
Devon Ryan64k wrote:

To my knowledge (there's basically no documentation that I've seen), the only way to get a lossy behaviour is by specifying --output-fmt-option lossy_names. You can do something with the auxiliary tags too I think (the required_tags option), but I've never looked into how that actually works.

ADD COMMENTlink written 3 days ago by Devon Ryan64k
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