gatk_pon: Make a Panel of Normals using the GATK toolkit
In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Construct a somatic Panel of Normals according to GATK best practices.

gatk_make_pon(
  bam,
  reference,
  vcf,
  outdir = "pon",
  intervals = NULL,
  remake = FALSE
)

gatk_GenomicsDBImport(
  vcf,
  reference,
  database,
  intervals = NULL,
  remake = FALSE
)

gatk_CreateSomaticPanelOfNormals(database, reference, vcf, remake = FALSE)

`bam`	one or more input sam/bam files
`reference`	a reference genome that was used during mapping of the sam/bam files
`vcf`	a variant call file, either one or more vcf to be merged into a database (for `gatk_GenomicsDBImport`) or an output vcf with Panel of Normals (for `gatk_make_pon` and `gatk_CreateSomaticPanelOfNormals`)
`outdir`	optional outdir an output directory for intermediate files
`intervals`	optional a character string or a file (one line per file) of genomic segments over which to operate. If not provided, these itnervals are derived from the reference `.fai` file.
`remake`	optional remake the output if it already exists
`database`	a name of the database file created by `gatk_GenomicsDBImport` and used in `gatk_CreateSomaticPanelOfNormals`.

gatk_make_pon is a convenience function that creates the Panel of Normals out of one or multiple bam files according to GATK best practices. The input bam files are first mapped using the gatk_Mutect2 in a tumour-only mode, the resulting vcf files are merged into a database using the gatk_GenomicDBIImport and then a the Panel of Normals is created using the gatk_CreateSomaticPanelOfNormals.

gatk_GenomicsDBImport merges multiple variant call files (vcf), such as those created by gatk_Mutect2, into a database. This database can be used to create a Panel of Normals using the gatk_CreateSomaticPanelOfNormals call.

gatk_CreateSomaticPanelOfNormals creates a Panel of Normals vcf out of a provided database. Panel of Normals are typically created out of multiple guranteed normal samples that use the same same sequencing technology as the tumour sample. Panel of Normals are used in the gatk_Mutect2 to inform the caller about technological errors and properties and also to filter out pre-existing variants.

bioDS/phyloRNA documentation built on Feb. 21, 2022, 3:28 p.m.