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Known Sites for GATK's BQSR for non-human data

Hello,

I am working on non-human data and want to use GATK's Haplotype caller to call variants. I am using the protocol that is listed here.

So far I have reached the indel realignment stage and want to do base recalibration next. Since I do not have known sites, this page in the GATK forum advises you to do an initial round of SNP calling on original un-recalibrated data.

Has anybody experience doing this? Is this initial calling done with UnifiedGenotyper on the indel realigned BAMs, or since I want to use Haploytype Caller downstream, should I use this module instead?

Thanks for your input!

Cheers,
Mika

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