tronflow-mutect2
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TRON-Bioinformatics
Nextflow pipeline for Mutect2 somatic variant calling best practices
Update PON best practice Nextflow pipeline according to the GATK documentation: - [(How to) Call somatic mutations using GATK4 Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2) - [Panel of Normals (PON)](https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON) Please note that the new...
* Separate gnomad files for germline filtering in MUTECT2 (gnomad_af_only_hg38) and contamination estimation in PILEUP_SUMMARIES (small_exac_common_3) to avoid Java heap out of memory error
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Nextflow pipeline for Mutect2 somatic variant calling best practices