Mutect2 genotype mode

Follow

Stefano Lise

• December 08, 2023 12:21

Hello, 

is there a way to run Mutect2 (version 4.4.0) in a purely genotype mode? I am aware of the force-calling mode (--alleles) but my understanding is that it will call at specified positions plus look for any additional variants. I would be interested (to hopefully limit the CPU time) in retrieving only the calls at specified positions in the vcf file. In previous versions there was an option -genotyping-mode GENOTYPE_GIVEN_ALLELES, is there anything equivalent? Many thanks for your help and for all the tools you provide.

Stefano

 

 

 

0

• 

  David Benjamin

  • December 18, 2023 19:58

  Stefano Lise There is not a mode to call only the given alleles and disable discovery of any other variation.  However, if your concern is compute time you can use the same VCF as both the --alleles argument and the -L (intervals) argument.

  1

  Comment actions Permalink

Please sign in to leave a comment.