Output file from samtools index is empty

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4.1 years ago

dave10808 • 0

Hello, I haven't been able to find anything related to this question. For some strange reason after indexing .BAM file the output .BAI file is empty. No error message is shown, neither the output itself is empty (the file is created after all, just empty).

samtools index filename.bam

Any ideas what might be the cause? My .BAM file is sorted and not corrupted.

BAI samtools BAM Index • 2.1k views

ADD COMMENT • link updated 4.1 years ago by cpad0112 21k • written 4.1 years ago by dave10808 • 0

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Can you post the output of this command file filename.bam?

ADD REPLY • link 4.1 years ago by GenoMax 154k

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Sure, here it is:

SRR12854173.sorted.bam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 63

ADD REPLY • link 4.1 years ago by dave10808 • 0

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can you please run samtools quickcheck on your bam file? Here is the manual: https://www.htslib.org/doc/samtools-quickcheck.html and if you have time, please try ValidateSamFile from picard on your bam.

ADD REPLY • link 4.1 years ago by cpad0112 21k

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