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Process and filter small variant data-frame to requirements

Source: R/wrangle.R
process_and_filter_small_variant_data.Rd

Processes small-variant data to comply with requirements for further analysis. The function:

  1. filters for variants that:

    • have a consequence in a pre-defined list (see details)

    • are present with depth > 0

  2. extracts NP ID and protein information from the P Dot-notation column

  3. adds columns to faciliate addition of annotation data

Usage

process_and_filter_small_variant_data(small_variant_df)

Arguments

small_variant_df

Data-frame of small variants

Value

processed and filtered data frame

Details

The following variant consequences are currently included:

  • frameshift_variant

  • inframe_deletion

  • inframe_insertion

  • missense_variant

  • missense_variant:splice_region_variant

  • splice_acceptor_variant

  • splice_donor_variant

  • splice_donor_variant:intron_variant

  • start_lost

  • stop_gained

  • stop_gained:splice_region_variant

  • stop_lost