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UnifiedGenotyper- problem when calling in chunks on reduced BAMs

totatota Posts: 3Member


Im trying to call variants using UnifiedGenotyper on ca 450 reduced bams in 100000 bp chunks. It works fine for some of the chunks, but for others I get the following error message:

ERROR MESSAGE: SAM/BAM nameOfBam.bam is malformed: Unexpected compressed block length: 1

Can anyone explain to me why there is a problem with a specific bam file when I call on for example chunk chr20:25400000-25500000 but not when I call on chunk chr20:10000000-10100000?

Thank you, Tota

Best Answers


  • totatota Posts: 3Member

    Thanks for your reply.

    I did generate the BAM using GATK -T ReduceReads. When I try to regenerate the index file using "samtools index", I get this message before the program terminates:

    $ samtools index reduced.bam bam_index_core] truncated file? Continue anyway. (-4)

    I'm surprised by this error message since it looks like the BAM is complete according to its LOG, which ends in these 4 lines:

    INFO 02:20:06,640 TraversalEngine - Total runtime 36955.17 secs, 615.92 min, 10.27 hours INFO 02:20:06,640 TraversalEngine - 4801933 reads were filtered out during traversal out of 71057279 total (6.76%) INFO 02:20:06,640 TraversalEngine - -> 3830446 reads (5.39% of total) failing DuplicateReadFilter INFO 02:20:06,640 TraversalEngine - -> 971487 reads (1.37% of total) failing UnmappedReadFilter

    Also, the BAM contains the EOF character indicating its not truncated. Any suggestions on how to solve this?

    Thanks, Tota

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