adding custom annotation to INFO or FORMAT field

ano1986ano1986 BelgiumMember


I use the CombineVariants tool (GATK v3.3) to combine variants called with Unified Genotyper and HaplotyperCaller for one sample into one .vcf. Is there a way to add a column in the INFO or FORMAT field that signifies from which .vcf (ug.vcf or hc.vcf) the variant originates. In my case it's not possible that the variant was present in both .vcf's

java -jar GenomeAnalysisTK.jar -T CombineVariants -R /home/ngs/data/tools/gatk/hg/broad_bundle_hg19_v2.5/hg19_chr1-y.fasta --assumeIdenticalSamples -V:ug ug.vcf -V:hc hc.vcf --genotypemergeoption PRIORITIZE -priority hc,ug -o ug_hc.vcf



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