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nanoporetech / pomoxis

Analysis components from Oxford Nanopore Research
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[bug] Running catalogue_errors then get 'ValueError: MD tag not present' #43

Closed yipukangda closed 3 years ago

yipukangda commented 3 years ago

I run catalogue_errors program with cmd:

catalogue_errors -t 20 -o variant ont.bam

And get an error message shows:

ValueError: MD tag not present

pomoxis version 0.3.4

cjw85 commented 3 years ago

The catalogue_errors program requires the MD tag to be present in the input bam file, this can be generated using samtools calmd: http://www.htslib.org/doc/samtools-calmd.html

yipukangda commented 3 years ago

The catalogue_errors program requires the MD tag to be present in the input bam file, this can be generated using samtools calmd: http://www.htslib.org/doc/samtools-calmd.html

it works, Thanks for helping.