phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description Usage Arguments Details See Also

Prepare sam/bam file from scRNAseq according to GATK best practices for further analysis, such as the SNV detection.

gatk_prepare(
  input,
  output,
  reference,
  vcf,
  barcodes = NULL,
  outdir = NULL,
  clean = TRUE,
  remake = FALSE
)

`input`	an input sam/bam file
`output`	an output sam/bam file
`reference`	a reference fasta (`.fas`) file to which the sam/bam file was mapped
`vcf`	a vcf file with known polymorphic sites
`barcodes`	optional file with cell barcodes to preserve
`outdir`	optional an output directory for intermediate files
`clean`	optional clean intermediate files
`remake`	optional remake the output if it already exists

This is a convenience function that chains individual GATK calls to prepare a mapped sam/bam file for further SNV detection. Following steps are performed:

optional FilterSamReadsTag– a barcode fitering step to preserve only high-quality cells
SortSam – sort reads according to coordinates
SplitNCigarReads – split reads around the N position in their CIGAR tag (see the GATK documentation for more information)
BaseRecalibrator – recalibrates the base quality scores after the SplitNCigarReads
ApplyBQSR – applies the recalibrated base quality scores from BaseRecalibrator

Note that in contrast to the GATK best practices for the RNAseq, the MarkDuplicates step is not performed as in scRNAseq, all sequences are barcoded.

GATK and GATKR6 for a binding to individual GATK functions, gatk_snv for another convenience function build on GATK calls

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