Need help with "Unified Genotyper" tool

Question: Need help with "Unified Genotyper" tool

4.3 years ago by

European Union

Hi there,

I would like to add the file 'dbsnp_137.hg19.vcf' to my GATK unified-genotyper analysis as option -D, how can I find this file directly on Galaxy and, if not, can I upload it from my computer in the option Get Data? Thanks a lot.

Tool name: Unified Genotyper
Tool version: 0.0.6
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/gatk_unified_genotyper/0.0.6
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/unified_genotyper

unified-genotyper • 1.2k views

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modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by mariano.avino • 0

4.3 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

you need to upload this file with the Galaxy upload tools, for example 'Get data', as you mentioned. If you are running your own instance, you can ask your administrator to put such files in a data library.

Cheers,

Bjoern

ADD COMMENT • link written 4.3 years ago by Bjoern Gruening ♦ 5.1k

4.3 years ago by

mariano.avino • 0

European Union

mariano.avino • 0 wrote:

Thank you for your answer.

I was able to upload my dbsnp file, however now I have another problem: my reference file and my dbsnp files are incompatible because they have different chromosome names. The reference one do not have the word 'chr' in front of the number and the mitochondrial one is called MT instead of M. My reference file is hg_g1k_v37 (the one from Galaxy). Is there any way I can find a dbsnp with the same names for the chromosomes of my reference file (maybe there is a way to get from Galaxy or somewhere)? I just would like to avoid an editing process on my big giga bam file. Thanks a lot again.

ADD COMMENT • link written 4.3 years ago by mariano.avino • 0

4.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A version of the dbsnp data that is a match for the for the hg_g1k_v37 reference genome build is available as a shared resource on the public Main Galaxy instance under Shared Data -> Data Libraries -> GATK. Choose the one for the reference genome "b37".

If working somewhere else, this is the source bundle location, with a description of contents:
http://www.broadinstitute.org/gatk/guide/article?id=1213

Hopefully this helps, Jen, Galaxy team

ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

wow it is exactly the answer I needed, great!

I am a newbie for everything and this helped me a lot. Thank you very much!

ADD REPLY • link written 4.3 years ago by mariano.avino • 0

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