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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,
BW
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,
BW