who can share the GATK PON file (better above 10 sample) , hg19 version?
Hi,dear all, we are using GATK Mutect2 to get the somatic mutations of the sample, while we have to create our own PON file, which we have to download the bam files of 1000g genome, call vcf and then make the PON file,
while it takes a lot of time to download(our band is not that widely), is that possible that anyone can share the file, great thanks and best wishes!
• 522 views
•
link
updated
by
finswimmer
•
written
by
dew •
•
written
by
dew •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Get both somatic and germline mutations from tumor only sample?
written by wormball •
-
Are there any repository for panel of normal for running Mutect2?
written by DareDevil
-
GATK Mutect2 tumor mode
written by cocchi.e89
-
Somatic variant calling mutect2 tumour only
written by cellulebioinfobiscem •
-
What is the different if I call germline SNP/Indel with mutect and HaplotypeCaller?
written by Makplus T
-
How to interpret the output of gatk?
written by Laven9 •
-
Mutect2 "somatic" variants with resistant tissue culture lines
written by shawn.w.foley
-
Variant calling on single sample Macaque WGS data - advice please
written by BioinfGuru
-
Mutect2 filtering log-odds (LOD) threshold
written by CY
-
Forum: MutSigCV question: Why V1.3 and V1.4 have great different result?
written by bioxujintian •
thanks for your post!
Sending the entire 1000 Genomes data via email will not be possible. Do you understand the size of the dataset? If you follow this from Steps 1-4, you will have the entire 1000 Genomes Phase III data in VCF / BCF format: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
End file size is ~15 GB
Plus, how would downloading from email consume any less bandwidth than downloading from the web?