VariantsToBinaryPed tool missing from GATK4?

Question

[gaelgarcia05]

Hi all,

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 VariantsToBinaryPed!

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

returns:

`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.

[chrchang523]

Any reason you aren’t using plink —vcf for this? plink 2.0 keeps track of ref/alt alleles if that matters to you.

[gaelgarcia05]

Hi @chrchang523 -- I haven't been able to get PLINK running on my computer, so I've decided to stick to GATK for now, as at least that one is running...

[chrchang523]

There are prebuilt Mac binaries; what problem occurs when you try to run them? I haven’t heard of anyone with OS X 10.7 or later having a problem getting started.

[gaelgarcia05]

Thanks @chrchang - I was able to get PLINK going after switching to my desktop in the lab.

Answer 1

[igor]

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?

If the tool is not listed in GATK4 documentation, it probably wasn't ported. Some tools were not ported.

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 VariantsToBinaryPed!

GATK shouldn't have any new software hassles. It's just a zip file that has to be uncompressed.

Will I have to install GATK3 to use this tool?

Yes. GenomeAnalysisTK.jar does not exist in GATK4 and that is why you are getting an error. Also, you command should include the path to the GenomeAnalysisTK.jar file unless you are running it from that directory.

can GATK3 and GATK4 coexist on my system?

Yes. When you uncompress them, they will each create a distinct directory.

[gaelgarcia05]

Thank you for your clear response, @igor. If I may add one more question -- why does this tool require a -R reference.fasta? It seems to me that it is not needed, as the VCF contains the location of the variants for the creation of the .bim / extended .map file. However, GATK returns an error if I don't provide a reference genome here.