Dear GATK team, I got my raw variant vcf output. Now I want to perform VQSR with those raw variants. Some VCF files in the resource bundle need to be downloaded for variant recalibration. I don't know why I can't access to the resource today. When I click into the "our public FTP server" link. Nothing showed up. It's quite weird because I just downloaded some dbSNP VCF files yesterday without even log-in. It didn't ask me for Username and Password. Sorry about the trouble. Looking forward to your reply.
I have two questions concerning the resource bundle. First, I'm trying to run MuTect 1.1.4, so which version of the resource bundle should I use (2.5 vs. 2.8, or some other one)?
Second, while I can access the ftp site via a web browser on the ftp://firstname.lastname@example.org/bundle , I am unable to ftp or sftp directly onto the site using sftp email@example.com , as instructed. I consistently get a Connection timed out/Couldn't read packet error. Is there some other username or address that I need to use?
Hi, It is becoming more and more difficult for us who are analyzing data in a transition period. After hg38 public release all the databases are updated with recent assembly. Now some people like us who are using GATK best practices facing a real problem to match our data with the databases. My basic question is when the supprotive files for hg38 are going to be available in your ftp site as a bundle.
I may have missed, but can you please give me information about the release version of GRCh37 (p13 or what) available in 2.5 and 2.8 bundle. Thanks in advance.
Hi all --
This should be a simple problem -- I cannot find a valid version of the Mills indel reference in the resource bundle, or anywhere else online!
All versions of the reference VCF are stripped of genotypes and do not contain a FORMAT column or any additional annotations.
I am accessing the Broad's public FTP, and none of the Mills VCF files in bundle folders 2.5 or 2.8 contain a full VCF. I understand that there are "sites only" VCF, but I can't seem to find anything else.
Can anyone link me to a version that contains the recommended annotations for indel VQSR, or that can be annotated?