Hi,

I am trying to merge 3 VCFs (one for each sample) into a single VCF, and I would like them to be listed in a specific order (proband, mother, father).

How can I specify this to GATK CombineVariants?

I've tried inputting the arguments in order, with the first variant given by me being proband. However, that didn't change anything. Any suggestions? My code is below.

VCFarray holds Father_VCF.vcf, Mother_VCF.vcf, and Proband_VCF.vcf

java -jar /opt/applications/gatk/3.3-0/GenomeAnalysisTK.jar \
   -T CombineVariants \
   -R ${fasta_path}chrRCRS.fa \
   --variant:father "${VCFDir}/${VCFarray[0]}" \
   --variant:mother "${VCFDir}/${VCFarray[1]}" \
   --variant:proband "${VCFDir}/${VCFarray[2]}" \
   -genotypeMergeOptions PRIORITIZE \
   -priority proband,mother,father \
      -o combinedPrioritized.vcf

The output looks like

##reference=file:///gpfs/home/quacht/MToolBox/data/chrRCRS.fa
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    `ID18_Father    ID18_Mother    ID18_Proband`
chrRCRS    107    .    G    A    .    PASS    AC=1;AF=1.00;AN=1;set=father    GT:CILOW:CIUP:DP:HF    1:0.912:1.0:48:1.0    .    .
chrRCRS    146    .    T    C    .    PASS    AC=2;AF=1.00;AN=2;set=proband-mother    GT:CILOW:CIUP:DP:HF    .    1:0.926:1.0:58:1.0    1:0.945:1.0:80:1.0
chrRCRS    152    .    T    C    .    PASS    AC=2;AF=1.00;AN=2;set=proband-mother    GT:CILOW:CIUP:DP:HF    .    1:0.916:1.0:51:1.0    1:0.941:1.0:74:1.0