Question: GATK Select Variants Reference Genome
0
gravatar for peve
23 months ago by
peve0
peve0 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

ADD COMMENTlink modified 18 months ago by Guy Reeves1.0k • written 23 months ago by peve0
0
gravatar for Jennifer Hillman Jackson
23 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 23 months ago by Jennifer Hillman Jackson25k
0
gravatar for supinderkr
18 months ago by
supinderkr10
supinderkr10 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 COMMENTlink written 18 months ago by supinderkr10

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 REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
0
gravatar for supinderkr
18 months ago by
supinderkr10
supinderkr10 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 COMMENTlink written 18 months ago by supinderkr10

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

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
0
gravatar for Guy Reeves
18 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k 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 COMMENTlink modified 18 months ago • written 18 months ago by Guy Reeves1.0k
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