diff --git a/README.md b/README.md index 4ebde8b..732a3f2 100644 --- a/README.md +++ b/README.md @@ -143,6 +143,19 @@ GENE | The `/gene` tag of the feature (if it existed) PRODUCT | The `/product` tag of the feature (if it existed) EFFECT | The `snpEff` annotated consequence of this variant (ANN tag in .vcf) +## Columns in TXT format + +Name | Description +-----|------------ +ID | Reference + Sample +LENGTH | Length of the reference +ALIGNED | Number of sites aligned to +UNALIGNED | Number of sites unaligned +VARIANT | Number of sites different from the reference +HET | Number of sites heterozygous or poor quality genotype represented with an n (`--minqual`) +MASKED | Number of sites masked in reference represented with an X (`--mask`) +LOWCOV | Number of sites low coverage in this sample represented with an N (`--mincov`) + ## Variant Types Type | Name | Example