Merge pull request #171 from dianacornejo/master

Added CADD and Loftee annotations
cumc · Oct 26, 2023 · 379ba00 · 379ba00
2 parents d587dc2 + 95d83bc
commit 379ba00
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Showing 2 changed files with 16 additions and 3 deletions.
diff --git a/admin/csg.yml b/admin/csg.yml
@@ -24,9 +24,9 @@ hosts:
  #$ -cwd
  #$ -S /bin/bash
  #{partition}
- module load Singularity
+ source ~/mamba_activate.sh
+ module load Singularity/3.11.4
  module load R/4.2
- export PATH=$HOME/miniconda3/bin:$PATH
  export SINGULARITY_BIND="/mnt/mfs/:/mnt/mfs/,/mnt/vast/:/mnt/vast/"
  set -e
  cd {cur_dir}

diff --git a/variant-annotation/vep.ipynb b/variant-annotation/vep.ipynb
@@ -218,11 +218,24 @@
  " --dir_cache ${dir_cache} \\\n",
  " --dir_plugins $VEP_PLUGIN_DIR \\\n",
  " --everything \\\n",
- " --plugin LoF,${human_ancestor},${conservation_file},${gerp_bigwig}\n",
+ " --plugin LoF,human_ancestor_fa:${human_ancestor},loftee_path:$VEP_PLUGIN_DIR,conservation_file:${conservation_file},gerp_bigwig:${gerp_bigwig} \\\n",
+ " --plugin CADD,snv=${cadd_snps} \n",
  " bgzip --keep ${_output[0]}\n",
  " tabix ${_output[1]}"
  ]
  },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "d8b7cf9d-d8ff-47a2-8784-3949c943d1e8",
+ "metadata": {
+ "kernel": "SoS"
+ },
+ "outputs": [],
+ "source": [
+ "## FIXME: Still not able to get indel CADD annotation working "
+ ]
+ },
  {
  "cell_type": "markdown",
  "id": "728ff640-3949-4d33-bedd-58da204fc0cc",