VCF to Bed file format using GATK

Question

[Sa]

Hi, I am trying to convert my VCF file to a bed file however am incurring some issues.

I am using the command suggested by GATK best practices for VariantsToBinaryPed however i KEEP on getting the message that -bin option has not been given eventhough it has.

Thank you so much for help in advance!

Answer 1

[chrchang523]

Is there any reason you need to use GATK for this? Just use "plink --vcf [filename] --make-bed".

[Sa]

Thank you so much for your help!

I was actually incurring a different error with the GATK command which I was able to fix. The problem was a simple mixup.