GATK: Mapping to the Genome Analysis ToolKit (GATK)

In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description

A group of functions that map to a functionality of the Broadinstitute's Genome Analysis ToolKit.

Usage

gatk_MarkDuplicates(input, output, remake = FALSE)

gatk_SortSam(input, output, remake = FALSE)

gatk_SplitNCigarReads(input, output, reference, remake = FALSE)

gatk_BaseRecalibrator(input, reference, vcf, table, remake = FALSE)

gatk_ApplyBQSR(input, reference, table, output, remake = FALSE)

gatk_IndexFeatureFile(vcf, remake = FALSE)

gatk_BuildBamIndex(input, remake = FALSE)

gatk_FilterSamReadsTag(input, output, tag, values, remake = FALSE)

gatk_MergeSamFiles(inputs, output, remake = FALSE)

gatk_FilterMutectCalls(input, reference, output, remake = FALSE)

gatk_GetSampleName(input)

Arguments

input	an input sam/bam or vcf file (in case of Mutect2 calls)
output	an output sam/bam or vcf file (in case of Mutect2 calls)
remake	optional remake the output if it already exists
reference	a reference fasta (.fas) file to which the sam/bam file was mapped
vcf	a vcf file with known polymorphic sites
table	a table with recalibration information
tag	a name of tag
values	one or multiple values of particular tag to keep
inputs	a vector of sam/bam files

Functions

• gatk_MarkDuplicates: Mark duplicate reads in SAM/BAM file. These reads are then marked with a SAM tag

• gatk_SortSam: Sort SAM or BAM file according to coordinates.

• gatk_SplitNCigarReads: Split reads that contains N in their CIGAR string

• gatk_BaseRecalibrator: Recalibrate the base quality score and outputs a table of new recalibrated values

• gatk_ApplyBQSR: Apply the base quality score recalibration according to the recalculated scores from the [gatk_BaseRecalibrator]

• gatk_IndexFeatureFile: Create an index for the Variant Coding File

• gatk_BuildBamIndex: Create an index for the bam

• gatk_FilterSamReadsTag: Filter sam/bam file according to tag and its value

• gatk_MergeSamFiles: Merge multiple sam/bam files

• gatk_FilterMutectCalls: Filter Mutect2's VCF output

• gatk_GetSampleName: Get a sample information (SM tag) out of input bam file.

See Also

GATKR6 a GATK binding in the form of R6 class, gatk_prepare, gatk_make_pon] and gatk_snv for a convenience functions utilizing the GATK calls

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