sampleSwaps: Identify sample swaps and similarities
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

sampleSwaps

R Documentation

Identify sample swaps and similarities

Description

Given a list BAM files, the function genotypes known SNPs and identifies potentially related samples. For the source of SNPs, see reference

Usage

sampleSwaps(
  bams = NULL,
  build = "hg19",
  prefix = NULL,
  add = TRUE,
  min_depth = 30,
  ncores = 4,
  ...
)

Arguments

`bams`	Input bam files. Required.
`build`	reference genome build. Default "hg19". Can be hg19 or hg38
`prefix`	Prefix to add or remove from contig names in SNP file. If BAM files are aligned GRCh37/38 genome, use prefix 'chr' to 'add'
`add`	If prefix is used, default is to add prefix to contig names in SNP file. If FALSE prefix will be removed from contig names.
`min_depth`	Minimum read depth for a SNP to be considered. Default 30.
`ncores`	Default 4. Each BAM file will be launched on a separate thread. Works only on Unix and macOS.
`...`	Additional arguments passed to `bamreadcounts`

Value

a list with results summarized

References

Westphal, M., Frankhouser, D., Sonzone, C. et al. SMaSH: Sample matching using SNPs in humans. BMC Genomics 20, 1001 (2019). https://doi.org/10.1186/s12864-019-6332-7

PoisonAlien/maftools documentation built on Nov. 5, 2024, 4:12 p.m.