closedFORlunch

My SNP VCFs actually have the AD field in the FORMAT section, not the INFO section. AD should be in the FORMAT section as it could be used for a...

Actually, AD is specified as both an INFO field AND a FORMAT field. The INFO version is presumably the sum of all the FORMAT ones, although I don’t see why...

But, yes, mine is in FORMAT. And it should appear as : ##FORMAT= . ?

The variant FORMAT record AD fields contain integers.... how would they need to be adjusted? 1 10583 . G A 201.31 RF;RF8.6 RFQUAL_ALL=2.76;STR_PERIOD=0;STR_LENGTH=0;QD=3.097;MQ0=25;MQ=46.104;GC=0.710;CRF=0.111;AC=\ 1;AN=2;DP=65;NS=1 GT:GQ:DP:MQ:PS:PQ:AD:ADP:AF:ARF:BQ:FRF:MC:MF:SB:RFQUAL:FT 1|0:201:65:51:10583: 100:16:76:0.211:0.074:37:0.198:0:0.000:0.244:2.7\ 6:RF The AD...

Well, it appears that just changing the header did the trick. Duphold is running now that I modified the snp.vcf to have ##FORMAT=

ok- will give it a shot Thank You