Tagged with #resource-bundle
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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://gsapubftp-anonymous@ftp.broadinstitute.org/bundle , I am unable to ftp or sftp directly onto the site using sftp gsapubftp-anonymous@ftp.broadinstitute.org , 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?

Comments (5)

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.

Comments (6)

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?

Comments (12)

I was wondering when you guys plan on updating the bundle to GRCh38?