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KFDRC GATK CNV Somatic Pair Workflow

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The Kids First Data Resource Center GATK CNV Somatic Pair Workflow is a direct port of the GATK best practices workflow WDL. Workflow for running the GATK CNV pipeline on a matched pair (normal sample optional). Supports both WGS and WES.

Generalized steps:

  • prepares a genomic intervals list with PreprocessIntervals
  • collects read coverage counts across the preprocessed intervals
  • collects counts of reference versus alternate alleles with CollectAllelicCounts
  • annotate the preprocessed intervals
  • denoises read coverage data against the PoN with DenoiseReadCounts using principal component analysis
  • plots the results of standardizing and denoising copy ratios against the PoN
  • incorporates copy ratio and allelic counts data to group contiguous copy ratio and allelic counts segments with ModelSegments using kernel segmentation and Markov-chain Monte Carlo
  • calls amplification, deletion and neutral events for the segmented copy ratios
  • plots the results of segmentation and estimated allele-specific copy ratios

Notes from GATK:

  • The intervals argument (input_intervals and/or input_interval_list) is required for both WGS and WES workflows and accepts formats compatible with the GATK -L argument. These intervals will be padded on both sides by the amount specified by padding (default 250) and split into bins of length specified by bin_length (default 1000; specify 0 to skip binning, e.g., for WES). For WGS, the intervals should simply cover the autosomal chromosomes (sex chromosomes may be included, but care should be taken to 1) avoid creating panels of mixed sex, and 2) denoise case samples only with panels containing only individuals of the same sex as the case samples).
  • Intervals can be blacklisted from coverage collection and all downstream steps by using the blacklist intervals argument (input_exclude_intervals and/or input_exclude_intervals_list), which accepts formats compatible with the GATK -XL argument. This may be useful for excluding centromeric regions, etc. from analysis. Alternatively, these regions may be manually filtered from the final callset.
  • The sites file (common_sites) should be a Picard or GATK-style interval list. This is a list of sites of known variation at which allelic counts will be collected for use in modeling minor-allele fractions.
  • To run gatk_funcotatesegments.cwl you must set run_funcotatesegments to True and provide at least funcotator_data_sources_tgz and funcotator_ref_version

Other Resources

dockerfiles: https://github.com/d3b-center/bixtools