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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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call somatic mutations #21

Open JingzhX opened 4 years ago

JingzhX commented 4 years ago

Hello,

Any tutorial on paired normal-tumor somatic mutation calling?

Thanks Jim

hsinnan75 commented 4 years ago

To call somatic mutations, please put "-somatic" in the command line, and specify the minimal ALT allele count (default is 10). We are still testing MapCaller on somatic mutation calling. If you have any suggestions, please let me know. Thank you!

JingzhX commented 4 years ago

It is very confusing. How to let the program know which sample is normal control and which is the matched tumor samples? It seems enabling "-somatic" doesn't change anything.

And how to do joint germline SNP calling for multiple samples?

hsinnan75 commented 4 years ago

Hi, MapCaller does not support multiple samples. I'll try to improve MapCaller to support that in the near future.