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  • How to preprocess SNP and SEQ

    Hello,

    I am newbie here and in SEQ data. I am trying to obtain tumor purity with THeta for SEQ and ASCAT for SNP. I would appreciate if anyone helps me how to produce the format of file.

    ASCAT example input:
    Tumor_LogR.txt: chrs pos s1 s2 ... s100 SNP1 1 1695590 -0.2096 -0.25
    Tumor_BAF.txt: chrs pos s1 s2 ... s100 SNP1 1 1695590 0 0.0694
    ...

    Additional question: It look like each number of SNP for a position has 100 records. Is there any reason to be 100?


    THeTa example input:

    #ID chrm start end tumorCount normalCount
    start_1_10001:end_1_570000 1 10001 570000 1075438 73714
    start_1_570001:end_1_106068800 1 570001 106068800 69021236 18495636
    start_1_106068801:end_1_110651200 1 106068801 110651200 4411350
    ...

    I have tried samtools+varscan and I have this format:
    chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content

    If I implement a segmentation of CBS(DNAcopy), then can I have such an example format?

    It would be a great help if you tell me how to do it. Thank you in advance.

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