On Tue, May 17, 2016 at 09:17:20PM +0000, Lin, Chih-Hsu wrote:
> During the conversion, BAM->CRAM->BAM, using samtools 1.3.1, I found the NM
> tags were changed. Does anyone have solution to that?
Can you give us a concrete example please; an alignment record along
with the relevant @SQ line so we can see what the reference is.
The reason for NM and MD changes is that CRAM doesn't explicitly store
these (although it could, it leads to larger files). Instead it uses
the reference to compute them on-the-fly. However we have seen a
number of cases where NM/MD in the original BAM file are incorrect,
due to bugs in aligners. This leads to changes after round-tripping
through CRAM.
So that said, are the NM values output by CRAM->BAM the same values
that samtools calmd generates? If so then this is fixing your data!
If not then we possibly have a bug that needs fixing.
Some have asked for a way to store the invalid data in CRAM
regardless. There is perhaps some (albeit twisted) logic to this as
it makes the validation of the data the responsibility of other tools
and not the file format itself. I experimented with this by writing
out all NM/MD, but it usually leads to 5-10% growth. A better
solution would be to check when they differ to the computed values and
only store them then, although that will slow up CRAM encoding
somewhat so I'm not convinced yet this is a problem in need of a
solution.
James
--
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