Phantom indels from HaplotypeCaller?

grafalgrafal MPI TuebingenMember

Dear GATK users and developers,

I am running HaplotypeCaller followed by ValidateVariants and the latter complains about variants that have called alternative allele without any observation for it.

ERROR MESSAGE: File /storage/rafal.gutaker/NEXT_test/work/4f/6f8738a66d1c9d12651b76b7ef8819/IRIS_313-15896.g.vcf fails strict validation: one or more of the ALT allele(s) for the record at position LOC_Os01g01010:6190 are not observed at all in the sample genotypes |
ERROR ------------------------------------------------------------------------------------------

Here is an example of site that ValidateVariant complains about:

LOC_Os01g01010 6190 . GT G, 0 . DP=4;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=14400.00 GT:AD:DP:GQ:PL:SB 0/0:4,0,0:4:12:0,12,135,12,135,135:4,0,0,0
LOC_Os01g01010 6192 . T . . END=6192 GT:DP:GQ:MIN_DP:PL 0/0:8:0:8:0,0,254

In general, it seems not dangerous so i am thinking of removing this check, but why is HaplotypeCaller finding phanotm variants is a mystery to me.

Thank you and

Best!
Rafal

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