US Holiday notice: this Thursday and Friday (Nov 25-26) the forum will be unattended. Normal service will resume Monday Nov 29. Happy Thanksgiving!

What's in the resource bundle and how can I get it?

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin
edited March 2013 in FAQs

1. Obtaining the bundle

Inside of the Broad, the latest bundle will always be available in:

/humgen/gsa-hpprojects/GATK/bundle/current

with a subdirectory containing for each reference sequence and associated data files.

External users can download these files (or corresponding .gz versions) from the GSA FTP Server in the directory bundle. Gzipped files should be unzipped before attempting to use them. Note that there is no "current link" on the FTP; users should download the highest numbered directory under current (this is the most recent data set).

2. b37 Resources: the Standard Data Set

  • Reference sequence (standard 1000 Genomes fasta) along with fai and dict files
  • dbSNP in VCF. This includes two files:
    • The most recent dbSNP release
    • This file subsetted to only sites discovered in or before dbSNPBuildID 129, which excludes the impact of the 1000 Genomes project and is useful for evaluation of dbSNP rate and Ti/Tv values at novel sites.
  • HapMap genotypes and sites VCFs
  • OMNI 2.5 genotypes for 1000 Genomes samples, as well as sites, VCF
  • The current best set of known indels to be used for local realignment (note that we don't use dbSNP for this anymore); use both files:
    • 1000G_phase1.indels.b37.vcf (currently from the 1000 Genomes Phase I indel calls)
    • Mills_and_1000G_gold_standard.indels.b37.sites.vcf
  • A large-scale standard single sample BAM file for testing:
    • NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam containing ~64x reads of NA12878 on chromosome 20
    • The results of the latest UnifiedGenotyper with default arguments run on this data set (NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.vcf)

Additionally, these files all have supplementary indices, statistics, and other QC data available.

3. hg18 Resources: lifted over from b37

Includes the UCSC-style hg18 reference along with all lifted over VCF files. The refGene track and BAM files are not available. We only provide data files for this genome-build that can be lifted over "easily" from our master b37 repository. Sorry for whatever inconvenience that this might cause.

Also includes a chain file to lift over to b37.

4. b36 Resources: lifted over from b37

Includes the 1000 Genomes pilot b36 formated reference sequence (human_b36_both.fasta) along with all lifted over VCF files. The refGene track and BAM files are not available. We only provide data files for this genome-build that can be lifted over "easily" from our master b37 repository. Sorry for whatever inconvenience that this might cause.

Also includes a chain file to lift over to b37.

5. hg19 Resources: lifted over from b37

Includes the UCSC-style hg19 reference along with all lifted over VCF files.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin

    Questions and comments up to August 2014 have been moved to an archival thread here:

    http://gatkforums.broadinstitute.org/discussion/4561/questions-about-the-resource-bundle

    Geraldine Van der Auwera, PhD

  • corlagoncorlagon germanyPosts: 7Member

    Hi Geraldine, It seems like I'm to stupid to understand your description on how to get the resource bundle... I want to test the suitability of MuTect for my analyses. From the respective download page, I got here to download the resource bundle. I followed the provided link at the top to get to the FAQ page "How can I access the GSA public FTP server?" which broad me to your ftp site "ftp.broadinstitute.org". There, I see 3 folders: "distribution", "incoming" and "outgoing". These contain numerous subfolders and files with cryptic or meaningless names. As I couldn't find anything related to that in the other comments, I'm probably missing something obvious here, but I can't figure it out. Could you please point me to the correct folder (or alternatively tell me which files are required by MuTect). Thanks in advance, c

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin

    @corlagon, make sure you use the login name specified in the document, which is necessary to access our team FTP server directly. Otherwise you end up in the general institute-wide server which has all that other content you don't want.

    Geraldine Van der Auwera, PhD

  • corlagoncorlagon germanyPosts: 7Member

    @Geraldine_VdAuwera said: corlagon, make sure you use the login name specified in the document, which is necessary to access our team FTP server directly. Otherwise you end up in the general institute-wide server which has all that other content you don't want.

    Ok, that was confusing... I expected the username to be required when I download something and as I just opened it via firefox, I wasn't asked for a username for login. Maybe it is better to provide the direct link? Opening "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle" will directly open the correct folder in the browser. Anyway - Thanks a lot for the fast help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin

    People have different ways of accessing FTP servers -- if you use a dedicated program like Filezilla, or go through a terminal, you don't use a direct link. But since it seems people increasingly use their browser for this, I'll add the link to the article.

    Geraldine Van der Auwera, PhD

  • bioSGbioSG Posts: 18Member

    Hello Geraldine,

    I'm looking for hg20 (GRCh38) updated bundle. Any future plans for release or I'm looking in the wrong place? Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin

    @bioSG Not in the near future, sorry. If the plan changes we'll make an announcement.

    Geraldine Van der Auwera, PhD

  • dmyersturnbulldmyersturnbull Stanford UniversityPosts: 3Member

    @Geraldine_VdAuwera‌, could you comment on why a GRCh38 bundle is not planned? Were there any problems using LiftOver, or is GRCh38 just not widely adopted enough? I'm asking because I'm interested in using UCSC's LiftOver to update the resource bundle for GRCh38 in my current work.

  • irtairta NIHPosts: 1Member

    Hi, I didn't find Mills_and_1000G_gold_standard.indels.b37.sites.vcf in the b37 directory. I did find Mills_and_1000G_gold_standard.indels.b37.vcf, which is what I imagine was meant. But since Mills_and_1000G_gold_standard.indels.hg19.sites.vcf exists in the hg19 directory I was just hoping you could confirm which file is the recommended one.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin

    Hi @irta,

    Sorry for the confusion; despite the name differences, the *b37.vcf file is equivalent to the *.b37.sites.vcf file. We'll fix the names in the near future for consistency.

    Geraldine Van der Auwera, PhD

  • SyedSyed IndiaPosts: 2Member
    edited November 13

    Hi ,

    I was trying to get indels.vcf from ftp but I am not able to point to correct folder for this task. I already logged in to ftp mentioned here https://www.broadinstitute.org/gatk/guide/article?id=1215 and the getting this folder structure.

    drwxrwxr-x 2 4452 wga 5 May 17 2011 1000GenomesExomes drwxrwxr-x 2 5844 1015 2 Aug 24 2011 1000GenomesLowPassPreliminaryIndelConsensusPhase1Release drwxrwxr-x 2 5509 1015 5 Jul 29 2011 1000GenomesPhase1ProjectConsensus drwxrwxr-x 8 5140 wga 8 Sep 16 13:54 1000GenomesValidation -rw-r--r-- 1 6303 1015 98304000 Apr 17 2014 1kg_gvfs.tar.bz2 drwxrwxr-x 4 depristo wga 4 Dec 8 2013 bundle drwxrwxr-x 2 depristo wga 3 May 15 2012 dbSNP135.no1000GProduction drwxrwxr-x 2 depristo wga 6 Nov 28 2011 DePristoNatGenet2011 drwxrwxr-x 2 4452 wga 4 Nov 15 2010 ESP drwxr-xr-x 2 6412 1015 8 Oct 24 16:49 foghorn140 drwxrwxr-x 2 7365 1015 16 Aug 5 00:13 forAlex drwxrwxr-x 2 5140 wga 3 Apr 3 2014 forBenR drwxrwxr-x 2 5140 wga 3 Mar 25 2011 forBrianBrowning drwxrwxr-x 2 depristo wga 5 Sep 21 2010 forDaniel drwxr-xr-x 2 6303 1015 4 May 7 2014 forIntel drwxrwxr-x 2 depristo wga 4 Feb 21 2012 forJustin drwxrwxr-x 2 5140 wga 6 May 4 2012 forLauraClarke drwxrwxr-x 2 6412 1015 7 Jan 23 2012 for_sakthi drwxrwxr-x 2 5140 wga 3 May 12 2014 forSynapDx drwxr-xr-x 3 6412 1015 3 Oct 14 18:19 for_szhang drwxr-xr-x 2 6412 1015 10 Jan 13 2012 forVineeta -rw-r--r-- 1 7211 1015 2141164 Jul 15 18:22 gatkdocs-3_1_v_3_2.zip drwxrwxr-x 2 5140 wga 3 Aug 12 2011 HLA drwxrwxr-x 2 5140 wga 10 May 22 2013 Liftover_Chain_Files drwxrwxr-x 2 7181 1015 6 Sep 14 2012 macarthur drwxrwxr-x 2 5844 1015 4 Sep 19 2011 MillsDevineIndelData drwxrwxr-x 2 5818 1015 5 Mar 18 2011 MNP drwxrwxr-x 2 5140 wga 5 Nov 19 2013 NA12878KB drwxrwxr-x 10 depristo wga 11 Oct 7 2011 old drwxrwxr-x 2 5140 wga 11 Nov 25 2013 PcrFreeTrios drwxrwxr-x 2 depristo wga 4 Jun 22 2011 readBackedPhasing drwxr-xr-x 4 6412 1015 4 Nov 16 2011 snpeffForGiulio drwxr-xr-x 2 6303 1015 5 Oct 1 17:55 travis drwxrwxr-x 2 5509 1015 3 Jan 19 2014 TrioSitesList -rw-rw-r-- 1 7211 1015 739681240 Oct 22 2013 tutorial_files.zip drwxrwxr-x 5 7211 1015 5 Sep 15 23:26 tutorials)**

    I am not sure where to go from here to download Indels.vcf and SNPs.vcf for ReAligner steps.

    Post edited by Syed on
  • SheilaSheila Broad InstitutePosts: 653Member, GATK Developer, Broadie, Moderator admin

    @Syed

    Hi,

    It looks like you clicked on the parent directory when you got to the server. Please try clicking on 2.8/ Then, you can choose your reference build (either b37/36 or hg19/18), where you will find what you are looking for.

    Good luck!

    -Sheila

  • SyedSyed IndiaPosts: 2Member

    I am not able to see any 2.8. at ftp://ftp.broadinstitute.org/ location.I did login with ftp client already but didn't able to do that.

  • SheilaSheila Broad InstitutePosts: 653Member, GATK Developer, Broadie, Moderator admin

    @Syed

    Hi,

    I am sorry, but I cannot see the same directories you are seeing. Can you please post the exact directories you see when you log in? Please tell me the exact directories you see the moment you log in.

    Thank you. Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,682Administrator, GATK Developer admin

    @Syed

    You had it right when you originally logged in with the FTP client. Look for the directory called "bundle". The directories @Sheila is referring to (2.8 etc) are in there. Let us know if you still can't find them.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.