Supporting reads about dysgu HOT 6 CLOSED

Hi,
There are a few metrics in the output that should be sufficient:
SU column in the INFO field is the 'support' for the event, a combination of PE, SR and WR
WR is the read count for number of 'within-read' SVs
SR is the number of split-reads
PE is the number of paired-end discordant reads

Hope that helps

from dysgu.

Hi @kcleal thank you for your reply. Unfortunately, I actually need something in the line of the RNAMES field generated by callers such as Sniffles and/or cuteSV. I would understand a "no, we won't implement it" if too much a bother :)

from dysgu.

I see, sorry I misunderstood, I can see how this would be useful. I think this could be incorporated as an option in a future release. Would you prefer the RNAME's to be dumped into the output vcf, or perhaps to a seperate csv file in the temporary directory?

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from dysgu.

Hi,
I've had a think about this feature and ran some quick tests, and I think it will be more difficult to implement efficiently than I first thought. The main problem is that paired-end reads end up consuming huge amounts of memory due to having to store all the query names of the reads. In the initial stages of analysis this can be quite problematic. I think I will put on hold trying to implement this for now.

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I think this option is very handy, just wondering if that can easily done for LR

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