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Cigar issue with no M or N between two I's when using --no-end-flt flag #392
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This is a known bug. I will fix it before the next release. For now, you can reduce the stringency level of picard. |
Fixed at the github HEAD. Let me know if it has issues. Thanks! |
Great, thanks Heng! |
@lh3 , Sorry to report the bad news, but I am still seeing this behavior after the latest release. The strange part of CIGARs are highlighted in the tag |
Hello @lh3: We're still seeing this issue with See below for stack trace. This is coming from a tool we use to identify dark regions, but it's built on Happy to provide any files that would help debug. We're just aligning one of the PacBio 1KG samples (
Can you help? Thanks! |
Hey Heng!
Working with Minimap2 I think I came across a weird edge case the other day that may be producing buggy behavior. This is using version 2.16. Given the following read:
After mapping to the human genome (hg38p12 - indexed with defaults) using the following command:
An alignment is produced which fails many picard tools operations (such as SamToFastq) with the following error:
From what I can tell it seems to be due to the following motif in the cigar:
However, if you take away the --no-end-flt flag this is no longer an issue. Any insight you have on whether this is a bug or not would be great!
Thanks,
Gavin
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