Which gatk version generates VCF version 4.1

Question

[taniamahmood38]

Dear all,

I want to prepare vcf file of 4.1 version. But GATK tool version 4 and above produces vcf version 4.2. Can anyone please share the link of GATK tool's version 3.8 or less. Any hep would be highly appreciated.

Thanks in advance

Answer 1

[Ram]

EDIT:

It looks like a bit of a complicated process to install GATK3.8. Here is how you need to do it:

1. Install gatk3.8 through conda: conda create -n gatk38 -c bioconda gatk then activate the env using conda activate gatk38
2. Get the JAR file from their Google cloud archive location (Exact file: https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2) using wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
3. Register the JAR using gatk3-register /path/to/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2. If you did not change directories in any step, you'll basically run gatk3-register GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2.
4. You're all set. Run gatk3 --help to ensure gatk3 works.

---

Did you try searching for "GATK 3.8" on Google? The fifth result I saw was: https://github.com/broadgsa/gatk

[taniamahmood38]

Thank you so much Ram, the conda solution worked for me. Thanks for your consideration.

[Ram]

Please accept my answer to mark this post as solved.

[taniamahmood38]

Done. I have marked it.

[taniamahmood38]

Sorry to ask but how can I produce VCF_v4.1 after downloading it form here because this folder does not contain any gatk file.

[Ram]

I'm sorry, I don't understand your question.

[taniamahmood38]

I mean I am unable to find any gatk script from this link https://github.com/broadgsa/gatk which you send me earlier. If it has no gatk script then what is the command to generate vcf file of version 4.1 from this.

Thanks

[Ram]

That's the github page. You should look under releases to find software that's ready for use. Here is the 3.8-1 release, for example.

Also, you can always install gatk 3.x using conda. conda install -c bioconda gatk

EDIT: Go with the conda solution, the GitHub source code route is a pain