Parameters for ABSOLUTE on WGS data
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5.5 years ago
shiyang93 ▴ 70

I want to use ABSOLUTE to estimate the purity of my WGS data. I have called the SNCA by BIC-seq and feed the seg data to ABSOLUTE. I have 2 questions: 1. Which platform should I use? I noticed there are 3 supported platforms: SNP_250K_STY, SNP_6.0 (default), Illumina_WES. None of them is WGS, so which should I use? Meanwhile I don't know the possible effects of choosing each paltform. 2. All of my samples successfully run and produced a Rdata and a pdf file. But there is one sample produced no pdf file. How can this phenomenon occurred? Does that mean that ABSOLUTE cannot find any solution for that sample? Which parameter could I change to find more solutions? (I changed the max.ploidy to 20 but an error occurred). Could anyone give me some advice? Thanks!

next-gen ABSOLUTE tumor purity ploidy • 1.3k views

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