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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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could using only tumor.bam extract logR and BAF? #103

Closed bio-rain closed 2 years ago

bio-rain commented 2 years ago

Hi, I have some tumor bem then I want to try ASCAT. I see I can use tumor file (logR and BAF) to generate ascat.output, but it does not seem to use tumor only to extract logR and BAF files. thanks

tlesluyes commented 2 years ago

Hi @bio-rain,

With sequencing data, ASCAT requires tumour/normal pairs to get an accurate measurement of logR. In addition, having matched normals help flag heterozygous SNPs that will be segmented.

Cheers,

Tom.