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For SNP calling, the documentation suggested to pool samples together to call Unified genotyper. My questions are:
I have samples for the same study done with exome-seq using Illumina platforms but some using GAII and some using HiSeq 2000 due to historical reasons. My question is: are they OK to be pooled together to call SNPs with Unified genotyper? How about the new HaplotyperCaller? Any concerns on that?
what about data from the same platform but using different exome-capture kits? My take-on for this is probably just the matter of where to look at the variants.
what about data from different platforms? e.g., some from Illumina, some from Ion torrent etc. Any concerns except for the needs of a common interval files for shared regions etc? Anybody tried before? Or just call SNPs for data from the same platform separately?
Thanks a lot for your help! Happy Thanksgiving!