Tumor mutation burden calculation based on bed file?
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26 days ago

Hi. I have created a maf file of somatic variants. Here is the bed file of our WES pipeline.

enter image description here

I want to calculate the TMB based on the total number of non-synonymous mutations and the total length of the exon coding region that the pipeline covered. I want to know which of the bed file list above can be used to get the total length of the exon coding region? The "_Regions.bed" or the "_Covered.bed"?

Below is the readme message

    * Covered.bed is used to assess coverage.

    * Padded.bed is used to call variant.
    * I have removed the first two lines of comments from the above two files, for instance
    ```
    browser position chr1:12081-12251
    track name="Covered" description="Agilent SureSelect DNA - SureSelect Human All Exon V6 - Genomic regions covered by probes" color=0,0,128 db=hg38
    ```
    You can download the BED files at https://earray.chem.agilent.com/suredesign/search.htm

    #### Information about the reagent kit
    * Design ID: S07604514
    * Name: SureSelect Human All Exon V6 r2
    * Category: SureSelect DNA
    * Species: H. sapiens (hg38)
    * Creation Date: 12-Jan-2016

    #### BED files' definition
    [design ID]_Covered.bed - This BED file contains a single track of the genomic regions that are covered by one or more probes in the design. The fourth column of the file contains annotation information. You can use this file for assessing coverage metrics.

    [design ID]_Padded.bed - This BED file contains a single track of the genomic regions that you can expect to sequence when using the design for target enrichment. To determine these regions, the program extends the regions in the Covered BED file by 100 bp on each side.

    Other categories: https://earray.chem.agilent.com/suredesign/help/Target_enrichment_design_files_available_for_download.htm#Files_for_custom_SureSelect_designs
TMB bed • 142 views
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