WGS hg19/hg38 Panel-of-Normals (GATK SV-CNV)
I am working on CNV calling through GATK latest guideline, in order to perform the analysis there's need for a Panel-of-Normals file that can be generated from other samples.
I was wondering if it possible to download these PoN files from some repository etc., I'm interested in both hg19 and hg38
Thank you very much in advance for any help!
• 2,380 views
•
link
written
by
cocchi.e89
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
GATK resource bundle alternatives
written by stlba •
-
Convert files made for b37 into hg19 human reference?
written by Manuel Sokolov Ravasqueira •
-
mosaic loss of chromosome - bioinformatics score
written by cocchi.e89
-
germline vs somatic CNV GATK calling
written by cocchi.e89
-
Panel of normals for Mutect2 GRCh37
written by nhaus •
-
monozygotic twins ped file specification
written by cocchi.e89
-
GATK somatic CNV results
written by cocchi.e89
-
GATK Mutect2 tumor mode
written by cocchi.e89
-
GATK Mutect2 tumor-segmentation table
written by cocchi.e89
-
Mutect2 somatic hemizygote variant on chrX
written by cocchi.e89
Hi, I would ask on the GATK support forum, and link back here when you do that. Thanks!
Hi,
I believe you can download 1000GP samples or PCAWG samples to do so (1st one is open, 2nd one require applying for an access).
In general I would pay attention to 2 parameters to match between your tumor samples and normal samples - 1) PCR-based or PCR-free sequencing (old samples tend to be PCR-based), 2) insert distance - different insert-distances create quite dissimilar coverage profiles.