Skip to content

v2.1
Compare
Choose a tag to compare
@nalcala nalcala released this 20 May 18:42
· 41 commits to master since this release
v2.1
759e42c
This commit was created on github.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Added new functionalities:

  • gatk4 support; gatk versions <=4 are still supported as in v1.0 but the pipeline is now not actively developed for them
  • conda environments, Dockerfiles, and Singularity files for gatk2, gatk3, and gatk4 and their profiles in nextflow.config
  • genotype mode (gatk4 only) on positions from a VCF (see help)
  • RNA-seq preprocessing for genotyping option (using gatk SplitNCigarReads and custom python script)
  • tn_file input mode now can include extra parameters specific to the genotype option (vcf for genotyping, and preprocessing of RNA-seq; see help)
  • allows multisample calling and genotyping; this requires tn_file input mode, and is automatically done when multiple rows in the tn_file have matching sample names
  • contamination estimation and filtering option (gatk4 only)
  • panel of normals option (gatk4 only)
  • now uses circleci 2

Minor changes:

  • parameter out_folder is now output_folder
  • parameter dbsnp is now known_snp
  • parameter bam_folder has been removed! now tn_file must specify the exact location, not the location relative to bam_folder
  • parameter gatk_version must be specified to use old version of gatk (default is 4)
  • prints params in log
Assets 2
Loading