I have a VCF header with the following number annotation for the AD field:
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
Where R means the field has one value for each possible allele (see: http://samtools.github.io/hts-specs/VCFv4.2.pdf).
However, when I try to run VariantRecalibrator and ApplyRecalibration on this VCF, I get the error:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Unable to parse header with error: For input string: "R", for input source: /path/to/myfile.vcf.gz
##### ERROR ------------------------------------------------------------------------------------------
When I reheader the VCF to fix the Number tag to Number=., the GATK modules work fine. Would it be possible to get this bug fixed? I'm working with a lot of large VCFs with this kind of header, and it's quite a headache to have to reheader these VCFs, when the header is actually a properly formatted VCF header.
Thanks!
Grace