make_a_table.py exception on BAM files without NH tag.

[hdangsoccer]

Hi, I encountered an exception from make_a_table,py script (discard_non_unique_mappings function) when using BAM files from HISAT2/samtools/picard, where some reads have no NH tag. According to HISAT2 manual, the tags are optional, so it is perhaps not a good assumption that NH and NM tags will always be there.
I got around the issue by adding a "try, except, continue" around the code to skip those reads.
Thanks for making the project freely available!
Regards,
Hong

[muffato]

Dear Hong,

Yes you're right, the script currently assumes both NH and NM tags are present. NH is used to detect unique reads, NM to indicate the number of mismatches; both are added by TopHat (which we used for the paper).
Does HISAT2 provide an equivalent tag to NH ? If so I can add that option to the script. Otherwise, the script can either (i) discard the reads where the tag is not present or (ii) not filter the reads (assuming they're all unique mappings).

Regards,
Matthieu

[hdangsoccer]

Hi, Matthieu, Yes, HISAT2 does output NH and NM tags for most read alignments, but not all. It can also incorporate SNP and indel information, so I am interested in how full HISAT2 index with SNP and alternative assemblies would perform for HLA compared to AltHapAlignR. Regards, Hong

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On Wed, Jul 25, 2018, 5:18 PM Matthieu Muffato ***@***.***> wrote: Dear Hong, Yes you're right, the script currently assumes both NH and NM tags are present. NH is used to detect unique reads, NM to indicate the number of mismatches; both are added by TopHat (which we used for the paper). Does HISAT2 provide an equivalent tag to NH ? If so I can add that option to the script. Otherwise, the script can either (i) discard the reads where the tag is not present or (ii) not filter the reads (assuming they're all unique mappings). Regards, Matthieu — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APHWmnE91Efxl5LItZ23pNIYN-_hNQe6ks5uKOCVgaJpZM4VgwkY> .