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mkirsche / Iris

A module for improving the insertion sequences of structural variant calls
MIT License
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Invalid read names error #11

Open zeeev opened 1 year ago

zeeev commented 1 year ago

I'm trying to run iris on long-read SV calls (read alignment based calling: sniffles/pbsv). When running iris via jasmine I get an error about the read name field being invalid. I'm guessing it's asking for a VCF info field? Most SV callers don't emit deadnames for records, so do you have any suggestions as to how to populate that field?

Skipping chrX:141968024:INS:pbsv.INS.65629 because of invalid read names field:  (time = 00:00:00:00.800)
Skipping chrX:142058136:INS:pbsv.INS.65632 because of invalid read names field:  (time = 00:00:00:00.800)
Skipping chrX:142058848:INS:pbsv.INS.65633 because of invalid read names field:  (time = 00:00:00:00.800)
Riccardo1274 commented 11 months ago

Hi, I'm having the same problem. I called the variants with pbsv and sniffles too. Did you manage to fix this error? It would be very helpful

6YuHao commented 8 months ago

I'm trying to run iris on long-read SV calls (read alignment based calling: sniffles/pbsv). When running iris via jasmine I get an error about the read name field being invalid. I'm guessing it's asking for a VCF info field? Most SV callers don't emit deadnames for records, so do you have any suggestions as to how to populate that field?

Skipping chrX:141968024:INS:pbsv.INS.65629 because of invalid read names field:  (time = 00:00:00:00.800)
Skipping chrX:142058136:INS:pbsv.INS.65632 because of invalid read names field:  (time = 00:00:00:00.800)
Skipping chrX:142058848:INS:pbsv.INS.65633 because of invalid read names field:  (time = 00:00:00:00.800)

Hello. Have you solved it yet. I need your help

Riccardo1274 commented 8 months ago

Hello, Yes, I have solved it. You need to call the variant including the 'rname' for each variant. If I understand correctly, this indicates which reads from the alignment the variant was found on. Sniffles has an option for this (--output-rnames), e.g: sniffles --input sample_aligned.bam --tandem-repeats tandem_repeats.bed --reference reference.fasta --output-rnames --threads 16 --vcf sample.vcf

I couldn't find anything similar with pbsv, so I couldn't use iris with it. I added cuteSV which is fast and has a similar option to sniffles. Hope this helps, Riccardo Rossi

6YuHao commented 8 months ago

Hello, Yes, I have solved it. You need to call the variant including the 'rname' for each variant. If I understand correctly, this indicates which reads from the alignment the variant was found on. Sniffles has an option for this (--output-rnames), e.g: sniffles --input sample_aligned.bam --tandem-repeats tandem_repeats.bed --reference reference.fasta --output-rnames --threads 16 --vcf sample.vcf

I couldn't find anything similar with pbsv, so I couldn't use iris with it. I added cuteSV which is fast and has a similar option to sniffles. Hope this helps, Riccardo Rossi

Thank you very much for your recovery, it helps me solve this problem