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
EDIT:
It looks like a bit of a complicated process to install GATK3.8. Here is how you need to do it:
conda create -n gatk38 -c bioconda gatk then activate the env using conda activate gatk38wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2gatk3-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.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
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.
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
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
Thank you so much Ram, the conda solution worked for me. Thanks for your consideration.
Done. I have marked it.
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