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