sampleSwaps {maftools} | 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

[Package maftools version 2.10.05 Index]