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List Variant Genotype

Special Note
  • The varlist function only lists calls for the minor allele, so if the reference is the minor allele then it will list reference "calls" and hets but will exclude homozygotes. This also filters out variants that are monomorphic in your population, and therefore if you only do varlist for one sample, only het calls are output. If you want to list for a single sample, it is recommended that you specify controls in your pedinfo file so that there is a ctrlmaf, and use the case only option to restrict the output to variants found in controls.

Command examples:

atav.sh --list-var-geno --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-var-geno: trigger list variant genotypes function.

--case-only: variants are only listed in the output when they are present in a case.

--mann-whitney-test: trigger to run variant Mann Whitney Test script downstream.

All the Command Options are available to use in this function.

Output:

genotypes.csv

Please check Output Columns for common columns.

sample.variant.count.csv

  • Sample Name
  • Total Sample Variant
  • Total Sample SNV
  • Total Ref SNV
  • Total Het SNV
  • Total Hom SNV
  • Total Sample INDEL
  • Total Ref INDEL
  • Total Het INDEL
  • Total Hom INDEL