Dan -
Is it possible that you are compressing GRCh37 alignments against the GRCh38
genome reference sequence ? Look for "hg19" in the original .bam header block.
I've noticed that not all of the previous samtools warnings and error messages
are provided yet by the new htslib versions of samtools.
- tom blackwell -
On Sun, 17 May 2015, Dan Greenfield wrote:
> Dear all,
>
> I encountered a problem converting a BAM file to CRAM and back again. This
> problem is exhibited on both samtools 1.1 and the latest download for
> samtools 1.2, each time reproduced from the first step.
>
> Steps to reproduce this:
> 1. download original BAM from EBI:
> ftp://ftp.sra.ebi.ac.uk/vol1/ERA172/ERA172924/bam/NA12878_S1.bam
> 2. convert to CRAM:
> samtools view -C -o NA12878_S1.cram -T hg38.fa NA12878_S1.bam
> 3. attempt to convert back to BAM:
> samtools view -b -o NA12878_S1.cram.bam -T hg38.fa NA12878_S1.cram
>
> Results from step 3: (no errors/warnings encountered in previous steps)
>
> Slice ends beyond reference end.
> Slice ends beyond reference end.
> ERROR: md5sum reference mismatch for ref 1 pos 248900092..248956422
> CRAM: 1ca5fd5ffe82936260309c85fc9b473b
> Ref : b47b43c987dbf1af96ca6d59061401c8
> Failure to decode slice
> [E::hts_close] Failed to decode sequence.
> samtools: error closing "NA12878_S1.cram": -1
>
> Here are the file sizes (note the cram file is actually bigger than the
> original bam):
> NA12878_S1.bam 121,691,186,161
> NA12878_S1.cram 125,386,599,695
> NA12878_S1.cram.bam 11,109,478,067
>
> Regards,
> Dan
>
>
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