Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

SV annotation using SVAnnotator in GenomeSTRiP2.0

SunhyeSunhye KoreaMember

Hi.
I got SV.vcf using GenomeSTRiP2.0 then annotated this file using SVAnnotator.
In AlleleFrequency.report.dat, POPULATION column contains "NA" not "Nation"

In AlleleFrequency.report.dat,

ID PLOIDY POPULATION AAF NALLELES
DEL_P0001_6 2 NA 0.226 124
DEL_P0001_12 2 NA 0.048 124
DEL_P0001_20 2 NA NA 124
DEL_P0001_27 2 NA NA 124
DEL_P0001_33 2 NA NA 124
DEL_P0001_36 2 NA 0.605 124
DEL_P0001_39 2 NA 0.000 124
DEL_P0001_40 2 NA NA 124
DEL_P0001_86 2 NA NA 124

In my pop.map

sample-00001      KOR
sample-00002      KOR
sample-00003      KOR
sample-00004      KOR
sample-00005      KOR
sample-00006      KOR
sample-00007      KOR
sample-00008      KOR

My population.map is wrong?
Otherwise, What is the problem?

And, to use GeneOverlapAnnotator, Where are the necessary files found (such as " gencode.v17.annotation.sorted.gtf ", "ucsc_gene_descriptions.dat") ?

Best Answers

Answers

Sign In or Register to comment.