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@d-cameron d-cameron released this 09 Sep 13:33
· 731 commits to master since this release
v2.6.0
45e2bc3

Somatic Calling

GRIDSS now has an offical tumour/normal somatic SV post-processing script.
This script has been developed for the Hartwig Medical Foundation cohort and is optimised for high quality sequencing data (40x normal, 100x tumour, ~500bp library fragment size, HiSeqX10/NovaSeq). It has been successfully used for clinical patient reporting in over 4,000 WGS patient samples.

The Hartwig hg19 GRIDSS panel of normals (PON) used in the somatic filter script can be downloaded from https://resources.hartwigmedicalfoundation.nl/.

Script Description
scripts/gridss.sh gridss driver script. Use this to run GRIDSS
scripts/gridss_somatic_filter.R GRIDSS tumour/normal somatic filtering script. Run this script on the GRIDSS output.
scripts/libgridss.R library used by gridss_somatic_filter.R
scripts/gridss.config.R somatic filtering configuration used for the Hartwig cohort
gridss_annotate_insertions_repeatmaster.R adds RepeatMasker annotations for VCFs annotated with gridss.AnnotateUntemplatedSequence

New docker images

  • A new GRIDSS docker image has been created. It will be available on Docker Hub as gridss/gridss:2.6.0 shortly.
  • A new combined GRIDSS/PURPLE/LINX docker image has been created. This docker image contains a stand-alone version of the Hartwig SV/CNV pipeline. It will be available on Docker Hub as gridss/gridss-purple-linx:latest shortly. Reference data required by this pipeline (including the GRIDSS PON) will be downloadable from https://resources.hartwigmedicalfoundation.nl/.

A GRIDSS/PURPLE/LINX bioarvix preprint will be posted soon.

Bug fixes

  • #213 also excluding indel assemblies from contributing to support interval
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