sc_mutations {FLAMES}R Documentation

FLAMES variant calling

Description

Candidate SNVs identified with filtering by coverage threshold, and allele frequency range.

Usage

sc_mutations(
  sce,
  barcode_tsv,
  bam_short,
  out_dir,
  genome_fa,
  annot,
  known_positions = NULL,
  min_cov = 100,
  report_pct = c(0.1, 0.9)
)

Arguments

sce

The SingleCellExperiment object from sc_long_pipeline

barcode_tsv

TSV file for cell barcodes

bam_short

(Optional) short read alignment BAM file. If provided, it is used to filter the variations. Variations in long-read data with enough short read coverage but no alternative allele will not be reported.

out_dir

(Optional) Output folder of sc_long_pipeline. Output files from this function will also be saved here. Use this parameter if you do not have the SingleCellExperiment object.

genome_fa

(Optional) Reference genome FASTA file. Use this parameter is if you do not wish sc_mutation to use the reference genome FASTA file from the sce's metadata.

annot

(Optional) The file path to gene annotation file in gff3 format. If provided as FALSE then the isoform_annotated.gff3 from sc_longread_pipeline will be used, if not provided then the path in the SingleCellExperiment object will be used.

known_positions

(Optional) A list of known positions, with by chromosome name followed by the position, e.g. ('chr1', 123, 'chr1', 124, 'chrX', 567). These locations will not be filtered and its allele frequencies will be reported.

min_cov

The coverage threshold for filtering candidate SNVs. Positions with reads less then this number will not be considered.

report_pct

The allele frequency range for filtering candidate SNVs. Positions with less or higher allele frequency will not be reported. The default is 0.10-0.90

Details

Takes the SingleCellExperiment object from sc_long_pipeline and the cell barcodes as barcode. Alternatively, input can also be provided as out_dir, genome_fa, annot, barcode.

Value

a data.frame containing the following columns:

The table is sorted by decreasing adjusted P value.

files saved to out_dir/mutation:


[Package FLAMES version 1.0.2 Index]