Entering edit mode
18 months ago
taniamahmood38
▴
60
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
Thank you so much Ram, the conda solution worked for me. Thanks for your consideration.
Please accept my answer to mark this post as solved.
Done. I have marked it.
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'm sorry, I don't understand your question.
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