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Custom Info disappears after CombineVariants step

akmgakmg strasbourgMember
edited May 2016 in Ask the GATK team

Dear GATK team,

After calling and annotation of my two vcf files (calling with gatkUG & VarScan on a same sample), I have an HGVS information in the INFO column, of type :

GATKUG :

chr12 25398284 . C T 52094.77 PASS hgvs=KRAS:NM_004985:exon2:c.35G>A:p.G12D,KRAS:NM_033360:exon2:c.35G>A:p.G12D,KRAS:NM_033360.3:c.35G>A:p.Gly12Asp,KRAS:NM_004985.4:c.35G>A:p.Gly12Asp;... GT:AD:DP:GQ:PL 0/1:3331,2745:6078:99:52123,0,65185

VarScan:

chr12 25398284 . C T . PASS hgvs=KRAS:NM_033360:exon2:c.35G>A:p.G12D,KRAS:NM_004985:exon2:c.35G>A:p.G12D,KRAS:NM_033360.3:c.35G>A:p.Gly12Asp,KRAS:NM_004985.4:c.35G>A:p.Gly12Asp;... GT:ABQ:AD:ADF:ADR:DP:FREQ:GQ:PVAL:RBQ:RD:RDF:RDR:SDP 0/1:75:1356:1354:2:3028:44.78%:99:0E0:75:1672:1671:1:3037

( "..." after hgvs information means there are other annotations )

When I want to combine the two vcf files with CombineVariants, this info disapears in certain lines of the VCF, without warning or error of GATK. Have you ever encountered this type of error ?

Thank you.

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