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vibansal / crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples
MIT License
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Poolsize = 1 #24

Closed arunkumarramesh closed 3 years ago

arunkumarramesh commented 3 years ago

Hello, Can CRISP be used to call variants in 1000 homozygous samples? So multi-sample but a pool size of 1. I know pool size influences the maf cutoff but I feel like the method should still be OK to use. CRISP is a lot faster in calling SNPs compared to other approaches for 1000 samples. The calls for the sites I have looked at exactly match variant calling with other approaches and Sanger based confirmation. Thanks! Arun.

vibansal commented 3 years ago

Yes, it can be used. It works well in diploid samples (pool size = 2).