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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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non-SV filtering #215

Open torakichi1219 opened 1 year ago

torakichi1219 commented 1 year ago

Hi,

After using smoove to extract SVs for the trio, we attempt to use slivar on them to extract denovo-SVs. For example, mom:0/0, dad:0/0 -> kid:0/1 or 1/1 as denovo-SV. I use DHFFC < 0.7 for filtering DEL and DHFFC > 1.25 for filtering DUP. Is there any filtering for the part without SV (the 0/0 part)? I would appreciate it if you could enlighten me.

best, tora

brentp commented 1 year ago

Hi sorry for the delay. I think using the DHFFC is the best filter, along with genotype.

torakichi1219 commented 1 year ago

Thank you. Now I will try to filter using DHFFC.