Hello,
I am reading the documentation of HaplotypeCaller in order to use this tool for "Single-sample all-sites calling on DNAseq (for -ERC GVCF cohort analysis workflow)".
The table in the middle of the page indicates that the default value of --output_mode is NA. However, in the details below are listed 3 possible values: EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES and EMIT_ALL_SITES.
Which one is used as the default?
Sincerely,
TF