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sambamba-merge: BAM file is not coordinate-sorted: read 'm[??7?m??`??' must be before read 'm150209_042724_42177R_c100779832550000001823165208251590_s1_p0/101549/11999_40392' (at virtual offset 879295/0)
(Files from here: ftp://ftp-trace.ncbi.nih.gov//giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/PacBio_MtSinai_NIST/CSHL_bwamem_bam_GRCh37)
I'm not sure if there are problems with the read lengths from pacbio bams, but samtools merge works fine. sambamba view on the file merged from samtools works great.
The text was updated successfully, but these errors were encountered:
Thanks for reporting, that's indeed a serious bug. Somehow I totally forgot about existence of large reads when I was adding on-the-fly indexing feature — should work now.
I get this error:
When I try to run this command:
(Files from here: ftp://ftp-trace.ncbi.nih.gov//giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/PacBio_MtSinai_NIST/CSHL_bwamem_bam_GRCh37)
I'm not sure if there are problems with the read lengths from pacbio bams, but samtools merge works fine.
sambamba view
on the file merged from samtools works great.The text was updated successfully, but these errors were encountered: