-l parameter : minimum sv length to be reported.

[MehmetGoktay]

Hi Fritz,

I would like to get even one single nucleotide deletions or insertions. When I set -l parameter to 1. It gets so slow. 15 hours was not enough even to process couple of thousands reads.

Normally if -l is higher than 5 it takes 20 min.

Is it normal?

Best,
Mehmet

[mschatz]

Yes, PacBio reads typically have a 10% to 15% error rate, which means an indel every 6 to 10bp. If you set -l to 1, Sniffles will have to consider millions and millions of potential variants, most of which are not real. We have successfully tested Sniffles with variants as low as 10bp but do not recommend going below that threshold. We have had some success using freebayes or samtools for variants below this, but this will be a future research project to fully flush out these ideas. Cheers, Mike

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On Wed, Aug 23, 2017 at 8:24 AM, MehmetGoktay ***@***.***> wrote: Hi Fritz, I would like to get even one single nucleotide deletions or insertions. When I set -l parameter to 1. It gets so slow. 15 hours was not enough even to process couple of thousands reads. Normally if -l is higher than 5 it takes 20 min. Is it normal? Best, Mehmet — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#25>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAL988AdGSeV4SqC6MAfmQj6gnGwfOsbks5sbBnpgaJpZM4O_7W-> .

[MehmetGoktay]

Thank you very much Mike.