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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