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Converting ModelSegments outputs for ABSOLUTE


I work on exome data to detect somatic variants. I identified the SNPs/Indels with Mutect2 and I followed the ModelSegments tutorial to detect CNAs. Now I want to convert the AF outputs I got with ModelSegments into AllelicCapSeg outputs to use them with ABSOLUTE.

For this purpose, I tried to use part of this pipeline on GitHub (unsupported/combine_tracks_postprocessing_cnv/combine_tracks.wdl) to convert the data with the function "convert_model_segments_to_alleliccapseg". I use as input files from ModelSegments.

However, I don't really understand in the script the utility of the following parameters to use as threshold values (Float ? maf90_threshold and Int ? min_hets_acs_results)?

Is there a better way to do this conversion?

Thank you

Best Answer


  • bshifawbshifaw Member, Broadie, Moderator admin
    edited July 1

    Hi @Lea_F ,

    This is one of the few workflows in the GATK repo we do not support. We can help you with questions on workflows outside of the "unsupported" directory.

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