infoVariantCalls: Information on variant-level calls
In timflutre/rutilstimflutre: Timothee Flutre's personal R code

infoVariantCalls

R Documentation

Information on variant-level calls

Description

Return some information to help in hard-filtering variant-level calls. See GATK's Best Practices tutorial (https://www.broadinstitute.org/gatk/guide/topic?name=tutorials#tutorials2806).

Usage

infoVariantCalls(
  x,
  type = "SNP",
  thresh.qual = 20,
  thresh.qd = 2,
  thresh.fs = 60,
  thresh.mq = 40,
  thresh.mqrs = -12.5,
  thresh.rprs = -8,
  thresh.hs = 13,
  thresh.dp = NULL,
  thresh.crs = NULL,
  thresh.pnb = NULL,
  thresh.bqrs = NULL,
  thresh.gc = NULL,
  thresh.hw = 7,
  thresh.hr = 6,
  thresh.ic = NULL,
  thresh.lrs = NULL,
  thresh.sor = NULL
)

Arguments

`x`	data.frame, e.g. from "bcftools query –format '%CHROM\t%POS\t%TYPE\t...'"
`type`	variant type
`thresh.qual`	exclude variant if QUAL < threshold
`thresh.qd`	exclude variant if QD < threshold
`thresh.fs`	exclude variant if FS > threshold
`thresh.mq`	exclude variant if MQ < threshold
`thresh.mqrs`	exclude variant if MQRankSum < threshold (must be negative)
`thresh.rprs`	exclude variant if ReadPosRankSum < threshold (must be negative)
`thresh.hs`	exclude variant if HaplotypeScore > threshold (must be positive, http://dx.doi.org/10.1038/sdata.2015.11)
`thresh.dp`	if NULL, exclude variant if DP > 3 * mean(DP) (https://www.biostars.org/p/110670/#110671)
`thresh.crs`	exclude variant if ClippingRankSum < threshold (must be negative)
`thresh.pnb`	exclude variant if PercentNBase < threshold (must be in [0,100])
`thresh.bqrs`	exclude variant if BaseQRankSum < threshold (must be negative)
`thresh.gc`	exclude variant if GC > threshold (must be in [0,1])
`thresh.hw`	exclude variant if HW > threshold (must be positive)
`thresh.hr`	exclude variant if HRun > threshold (must be positive, http://dx.doi.org/10.1038/sdata.2015.11)
`thresh.ic`	exclude variant if InbreedingCoeff > threshold
`thresh.lrs`	exclude variant if LikelihoodRankSum < threshold (must be negative)
`thresh.sor`	exclude variant if SOR > threshold (must be positive)