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When the majority of tumor genome is doubled, the origin will be AABB, or AAABBB.
The genotype for the origin is determined using a global maximization of likelihood approach, to map as many observed data point to the theoretical canonical positions as possible.
Both indels and SNVs should be contained in one file for each tumor/normal pair. s CNA analysis CHAT provide two types of units of DNA segments: fixed SNP marker bins and natural CNA discovery (by circular binary segmentation). All the details can be found in the documentation files, but there are several things need to be paid attention to particularly.
User needs to create two directories: BAF/ and LRR/ with writing and reading privileges, save txt files for each of the 22 chromosomes in these directories with names chr N.txt, N=1,2,...22.
The columns for BAF and LRR files are: SNP id (optional), chromosome, position start, position end (optional), tumor_1, normal_1, tumor_2, normal_2, ...
To note, in BAF files, the identifier used in real file for tumor_i and normal_i should be exactly the same as those used in LRR files.
In other words, the first line for every BAF file and every LRR file should be identical.