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Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
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Filtering of CNVs/SV annotated vcf file #789

Closed ashwini06 closed 2 years ago

ashwini06 commented 3 years ago

The vep annotated outputs of CNVkit ends up with a huge list of annotations. For eg: /home/proj/long-term-stage/cancer/UMI_analysis_runs_APJ/cancer_test_datasets/panel_Tonly/cnv_tonly_wantedjay/analysis/vep/CNV.somatic.cnv_tonly_wantedjay.cnvkit.all.filtered.pass.vcf.gz

As of now, everything works and vep successfully output vcfs. But there should be a different strategy to deal with CNVs and structural variants, where final vep annotated VCFs INFO field looks readable and shorter.

Current affected rule if snakemake workflow related

https://github.com/Clinical-Genomics/BALSAMIC/blob/master/BALSAMIC/snakemake_rules/annotation/vep.rule

ashwini06 commented 2 years ago

From BALSAMIC v9.0, removed vcfanno and COSMIC from SV/CNV annotations. This is no more an issue.