Inquiry Regarding Somatic Analysis and Normal Sample Requirement

Inquiry Regarding Somatic Analysis and Normal Sample Requirement

1

Dear All,

I have two questions:

  1. I plan to perform somatic analysis on 10 different tumor BAM files to determine the SNPs, indels, and CNVs. Is it necessary to have 10 distinct normal files corresponding to each tumor BAM file, or can I use a single normal file for all 10 BAM files?

  2. If I don’t have a normal file and still want to perform somatic analysis, is there a solution to do it without requiring a normal sample?

Best regards,


somatic


germline


bioinformatics


ngs

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updated 2 hours ago by

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written 22 hours ago by

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10

The normal sample is used to know the expected healthy genotype, to distinguish germline from somatic variants, to filter artifacts, and so on. GATK team has a detailed explanation here. If your tumor samples come from different organisms, then yes, having 10 corresponding normal files will definitively increase the confidence of the variant calling, as the process will permit to have matched calls (tumor-normal) and to filter for technical issues (building a so called Panel of Normals).

While it’s possible to perform somatic variant calling without a matched normal, for example using Mutect2 in tumor-only mode, this is discouraged. Tumor cells could be subjected to many alterations, leading to a strange reads distribution across variants. You’ll see for sure an higher number of variants called, as many of them will likely be misclassified germline variants and/or technical biases which are nearly impossible to distinguish from true signals.


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