Comments (2)
MariaNattestad
commented on May 20, 2024
Sorry we didn't answer this issue sooner. No, you do not need to sort and index any bam files, and in fact I would not recommend it because DeepConsensus assumes that the inputs are in the original order that ccs and actc output. Changing that order by sorting might cause some data to be skipped during processing. We'll take a look and see if it's possible to turn off that warning, which I'm guessing is from pysam that we use for parsing the bam files.
from deepconsensus.
jelber2
commented on May 20, 2024
Ok thank you! I have not noticed anything with data being skipped, but maybe I was not looking carefully enough.
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Related Issues (20)
- Lower number of >Q30 average quality reads for v1.1 compared to v0.3 HOT 10
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