GATK Select Variants Reference Genome

Question: GATK Select Variants Reference Genome

2.1 years ago by

peve • 0

peve • 0 wrote:

Hi,

I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, but I'm having trouble with the Reference Genome input. I'd been using the Galaxy-supplied ce10 genome, but this tool doesn't let you use those as inputs. I've tried uploading the ce10 to my history, but I can't seem to get the tool to recognize the file as a reference genome. Is there a way to do this, or should I just download my own instance of Select Variants?

Thanks, Eve

build select variants genome gatk custom • 1.2k views

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modified 19 months ago by Guy Reeves • 1.0k • written 2.1 years ago by peve • 0

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Double check that the ce10 Custom reference genome is both formatted correctly and has the datatype "fasta" assigned. Certain tools will require that database is also assigned. Go forward and create a Custom Build to do this, making sure to name the custom genome/build something different than "ce10" - database names must be unique on any single instance.

How to:

Please be aware that the GATK tool at http://usegalaxy.org have been deprecated and may error even after this is all correct (for a variety of reasons). Should this occur, use a local or cloud Galaxy with the latest GATK tool repository installed.

Using Galaxy choices:

Best, Jen, Galaxy team

ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

supinderkr • 10

supinderkr • 10 wrote:

Hi this is my first time using galaxy and when i run my program all my mutants were showing error like this 36 Select Variants on data 3 and data 31 (log) error An error occurred with this dataset: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/581/15581989/_galaxy_tmp -Xmx7680m -Xms256m

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR A USER ERROR has occurre</h5>

35 Select Variants on data 3 and data 31 (Variant File).

Please suggest as I am new to sequencing as well and I used the workflow available from lab. Please help

ADD COMMENT • link written 19 months ago by supinderkr • 10

Hello,

All GATK tools at http://usegalaxy.org have been deprecated and are no longer supported. I don't think that the tool authors of the updated GATK tools in the Tool Shed (for a local or cloud Galaxy) are supporting these tools anymore either, due to licensing and other complications.

Instead, we suggest using alternative methods/tools for variant analysis. Please see the tutorials here: https://galaxyproject.org/learn/

Thanks!

ADD REPLY • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

supinderkr • 10

supinderkr • 10 wrote:

Hi Jen

Thanks a lot for your reply. Please suggest which tool i should use for variant analysis available in galaxy because I tried to use GATK but it didn't worked so please suggest as this is my first time and i am new to both sequencing and galaxy.

Thanks!

ADD COMMENT • link written 19 months ago by supinderkr • 10

For methods/tools for variant analysis, please see the tutorials here: https://galaxyproject.org/learn/

ADD REPLY • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

HI supinderkr

While almost all GATK tools are more trouble than they are worth in galaxy. I do find the 'select variants' tool to be useful and it works fine for me. I am sure that if you make your ref sequence compatible for galaxy (or get an FTP file from some source) and it matches exactly the one used to generate the vcf it will work. other options are NGS: VCF Manipulation -> VCFselectsamples OR VCFfilter (on use galaxy)

or 'SNPsift' (if you have your own galaxy instance) works great for me. CHeers Guy

ADD COMMENT • link modified 19 months ago • written 19 months ago by Guy Reeves • 1.0k

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