Hello, I was trying to download the resource bundle and using the credentials given on the website. Username: gsapubftp-anonymous and password is empty. Unfortunately I am not able to download files. Following is the error for most of the cases: 550/tutorials/workshops/GATKbasic: no such file or directory. Is there any way to download resource bundle? Thank you
Hi GATK Team,
I am Mia Yang. Would like to ask you some questions regarding the resources from GATK bundle.
(1) Is there any differences between the original files (HapMap, 1000G, Mills, etc..) and the one that we can download directly from the GATK bundle? And are these resources compatible with other variant re-calibration tools available out there?
(2) I can see that there are some labelled with hg19 at the back of the file names. Does this means that the files are only compatible with hg19 genome or it is optimized for hg19 and not the others (example hg38 etc..)?
Thank you in advance and have a nice day! =)
Dear GATK team,
Good day. I would like to ask about few things regarding the GATK bundle provided at ftp://ftp.broadinstitute.org/bundle/2.8/hg19/.
From the FTP site, there are few variant file (.vcf format) associated with 1000G, Mills, dbSNPs etc. I would like to ask about the differences between them with the original file provided by their original sources. By "hg19", does that meaning all the resource bundles are optimized for hg19 reference genome? How is the files provided at the bundle differs from the original files?
Thank you in advance.
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?