Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.
1.
I have some samples, comprised of liver cirrhosis, dysplastic nodules, early HCC, progressed HCC.
All samples don't have paired normal tissue.
So, I am wondering what PriorF will be used in cirrhosis, dysplastic nodules, and early HCC. (Progress HCC may be 0.7)
Can you recommend ?
2.
What maf are used to consider germline mutation in public SNPdb (1000g, exac)
Is right snv 1e-5, indel 1e-6 ??
Hi, thanks for the useful tools.
1. I have some samples, comprised of liver cirrhosis, dysplastic nodules, early HCC, progressed HCC. All samples don't have paired normal tissue. So, I am wondering what PriorF will be used in cirrhosis, dysplastic nodules, and early HCC. (Progress HCC may be 0.7) Can you recommend ?
2. What maf are used to consider germline mutation in public SNPdb (1000g, exac) Is right snv 1e-5, indel 1e-6 ??