cancerhotspots: Genotype known cancer hotspots from the tumor BAM file

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Genotype known cancer hotspots from the tumor BAM file

Description

'cancerhotspots' allows rapid genotyping of known somatic variants from the tumor BAM files. This facilitates to get a quick overlook of known somatic hot-spots in a matter of minutes, without spending hours on variant calling and annotation. In simple words, it fetches nucleotide frequencies of known somatic hotspots and prioritizes them based on allele frequency. Output includes a browsable/sharable HTML report of candidate variants. Known cancerhotspots for both GRCh37 and GRCh38 assemblies (3180 variants) are included. This should be sufficient and cover most of the known driver genes/events. See Reference for details.

Usage

cancerhotspots(
  bam = NULL,
  refbuild = "GRCh37",
  mapq = 10,
  sam_flag = 1024,
  vaf = 0.05,
  t_depth = 30,
  t_alt_count = 8,
  op = NULL,
  fa = NULL,
  browse = FALSE
)

Arguments

bam	Input bam file. Required.
refbuild	Default "GRCh37". Can be "GRCh37", "GRCh38", "hg19", "hg38"
mapq	Map quality. Default 10
sam_flag	SAM FLAG to filter reads. Default 1024
vaf	VAF threshold. Default 0.05 [Variant filter]
t_depth	Depth of coverage threshold. Default 30 [Variant filter]
t_alt_count	Min. number of reads supporting tumor allele . Default 8 [Variant filter]
op	Output file basename. Default parses from BAM file
fa	Indexed fasta file. If provided, extracts and adds reference base to the output tsv.
browse	If TRUE opens the html file in browser

References

Chang MT, Asthana S, Gao SP, et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat Biotechnol. 2016;34(2):155-163. doi:10.1038/nbt.3391

See Also

cancerhotspotsAggr

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