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Default value of --output_mode in HaplotypeCaller

timflutretimflutre Montpellier, FranceMember

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?



Best Answer


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