Generate VCF version 4.1 using GATK version 4

Question

[taniamahmood38]

Dear all,

I want to make vcf file of version 4.1 using gatk 4.0. I have tried using the command

./gatk HaplotypeCaller -R ref.fna -I sample.bam -O sample.vcf

But this generated the vcf 4.2 version file. Someone please let me know the exact command to generate vcf of version 4.1

Thanks in advance

Answer 1

[Ram]

I don't think you can, v4.1 is pretty old. We're already discussing a solution to this problem in a previous thread of yours, I don't see why you needed to open a new thread.

[taniamahmood38]

Really sorry! Actually previous question was a bit different. There I needed the previous gatk version to make vcf4.1 and here I want to use gatk4 for this purpose as I am still unable to find the gatk 3.8 or less version.

[Ram]

I see it this way: Your underlying problem is that you need VCFv4.1 and you need to use GATK to get one. You've opened two posts for two different versions of GATK.

I've also edited your title - using all caps online is akin to yelling in real life. You wouldn't yell at strangers in a professional setting, would you?

[taniamahmood38]

Extremely sorry, it was by mistake that I used all caps.

[Ram]

OK, no problem. I've fixed it for you. I should have given you the benefit of the doubt that it was an accident, I apologize for my harsh tone.

[taniamahmood38]

No its totally fine, thanks alot. You helped me a lot and the conda solution you told me here worked for me.