I've been prepping my data to input to GATK's Variant Manipulation Tool
VariantsToBinaryPed , but I just realized that GATK4 doesn't list this tool in its documentation. It is only under the GATK3 documentation. Is there a reason for this?
A bit of background - I need to convert my VCF and accompanying family info into PLINK's binary ped file(set),
.bed / .bim / .fam to check for pedigree errors using KING.
I was able to install GATK4 after the usual new software hassles - and I'm worried I'll have to install GATK3 instead to actually use
Running the example in the documentation (which I just realized is under GATK3):
java -jar GenomeAnalysisTK.jar \ -T VariantsToBinaryPed \ -R reference.fasta \ -V ~/MIPS_CSE/MIPS-02-13-18.vcf.bgz \ -m ~/MIPS/03_IdentityCheck/KING/targeted_seq_ped.fam \ -bed output.bed \ -bim output.bim \ -fam output.fam
`Error: Unable to access jarfile GenomeAnalysisTK.jar`
Will I have to install GATK3 to use this tool? If so, can GATK3 and GATK4 coexist on my system?
Thanks for any info.