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FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data
BSD 3-Clause "New" or "Revised" License
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Can I use already mapped and SNP calling VCF to do OptiType? #21

Closed cenielyj closed 8 years ago

cenielyj commented 8 years ago

This is Yijia Li from Yunnan Province Stem Cell Bank, China. We are very interested using your OptiType to do HLA typing. However may I ask if I can use already mapped and SNP calling VCF to do that without using the original fastq file? Thanks very much.

andras86 commented 8 years ago

Dear Yijia, It's not possible with OptiType. I suggest you look into HLA*IMP:02, SNP2HLA or HIBAG, but beware the limitations of resolving HLA genotypes from SNP data alone.