Output file from samtools index is empty
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.
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dave10808 •
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Can you post the output of this command
file filename.bam?Sure, here it is:
can you please run
samtools quickcheckon your bam file? Here is the manual: https://www.htslib.org/doc/samtools-quickcheck.html and if you have time, please tryValidateSamFilefrom picard on your bam.