Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Finding mutations in MiSeq data? gglike Illumina/Solexa 3 07-19-2017 03:17 AM
Have any of you tried the data of LSC paper? dis Pacific Biosciences 8 02-06-2013 04:30 PM
Review paper about quality issues in RNA-seq data?? paulig Literature Watch 2 03-27-2012 07:38 AM
Re-map data of Cufflinks paper by Trapnell et al. Tefina RNA Sequencing 4 08-25-2011 01:09 AM
New Paper: High Quality SNP Calling Using Illumina Data at Shallow Coverage nmalhis Bioinformatics 0 03-01-2010 02:40 PM

Thread Tools
Old 01-29-2020, 04:42 PM   #1
Junior Member
Location: Australasia

Join Date: Jan 2020
Posts: 1
Default Need help finding data from Google's DeepVariant paper

Apologies if this is not the usual type of question posted here.

I'm a postgraduate student trying to understand Google's DeepVariant paper, and a step in the process is trying to run VQSR and seeing how it compares with DeepVariant. The authors have kindly provided their GATK code:

I see the output of the variant calling step is a file called gatk3-raw.vcf.gz

Does anyone know where I might be able to find this file? The paper says "All data used in this manuscript is publicly available from Genome in a Bottle or the Mouse Genome project, with the exception of 35 NA12878 WGS replicates from the Verily sequencing laboratory, which were licensed from Verily for the current study and are not publicly available."

I went to the GIAB website and couldn't easily find it.

If that's not available, I can just recreate the files by calling haplotype caller. But I run into another problem since I can't find the input BAM file either. All I know is that they refer to it as "HG002_NIST_150bp_50x.bam". I'm not familiar with these abbreviations, so if anyone can guess where I might be able to find this dataset, I would be very grateful!

Last edited by Sonic20; 01-29-2020 at 10:00 PM.
Sonic20 is offline   Reply With Quote

data, sequencing, variantcalling

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:51 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO