Output file from samtools index is empty
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6 weeks 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 • 274 views
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Can you post the output of this command file filename.bam?

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Sure, here it is:

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

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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.