Question: Indels.vcf and SNPs.vcf from GATK ftp.
0
gravatar for always_learning
4.4 years ago by
Doha, Qatar
always_learning960 wrote:

Hi All,

I was trying to get indels.vcf from ftp but I am not able to point to correct folder for this task. As mentioned here https://www.broadinstitute.org/gatk/guide/article?id=1213 . 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. I was able to download these files from here already. but not getting this time. :( :(

gatk vcf • 1.6k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by always_learning960
1
The files you're looking for are in "bundle" folder if I remember correctly.
ADD REPLYlink written 4.4 years ago by iraun3.5k

But its not working this time. I checked "bundle" folder already. 

ADD REPLYlink written 4.4 years ago by always_learning960

Maybe the server was full. Now I'm able to get the files.
 

ADD REPLYlink written 4.4 years ago by iraun3.5k
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