[svtoolkit-help] Regarding Benchmark data and for structural variation other than deletions

[Ankita i. <an...@ig...>]

My queries are -

(i) I don't understand what are benchmark datasets in svtoolkit folder ? In
benchmark folder they have test vcf files. But i have used it for another
set of samples, what is benchmark data for them? That's why everytime on
running discovery.sh script i got error for differing with benchmark
dataset.

(ii) How can i find/discover duplications even without genotyping them
using Genome STRip (as i far i understand Genome STRip also works for
genotytping deletions), is there any script available to find duplications
using Genome STRip?




-
Regards
Ankita
DST Inspire Fellow (Graduate Student)
Lab no 604A
G.N. Ramachandran Knowledge Center for Genome Informatics
Institute of Genomics and Integrative Biology (CSIR)
North Campus DU, Near Jubliee Hall
Delhi - 110007


http://igvbrowser.igib.res.in