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UW-GAC / wgsaparsr

Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.
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reorganize columns of parsed output files #75

Closed jaind closed 5 years ago

jaind commented 6 years ago

The following columns, in that order, should always be the first set of columns to be reported in all parsed output files

  1. CHROM
  2. POS
  3. REF
  4. ALT
  5. FILTER
  6. chr_hg19
  7. pos_hg19
  8. alt_hg19
  9. ref_hg19
  10. ref_hg19_equals_ref_hg38
  11. rs_dbSNP150 ( or equivalent of rsID in future WGSA release)

For indels, the two columns below should follow next to the top eleven columns

  1. focal_snv_number
  2. indel_focal_length

For dbNSFP annotations the three columns below should follow next to the top eleven columns

  1. aaref
  2. aaalt
  3. Ensembl_geneid