verIndel: Verify Indel alignments

In hubentu/VarReviewer: Variant Reviewer

Description

Verify Indel alignments

Usage

verIndel(range, Ref = NULL, Alt = NULL, bam,
  genome = BSgenome.Hsapiens.1000genomes.hs37d5, mapq = 20,
  baseQ13 = NULL, trim.softclip = FALSE)

Arguments

range	A Ranges object.
Ref	Reference allele.
Alt	Alt alleles.
bam	BAM file.
genome	Reference genome file or BSgnome object.
mapq	mapping quality score.
baseQ13	base quality score.
trim.softclip	whether to realign softclip reads.

hubentu/VarReviewer documentation built on June 7, 2019, 12:48 a.m.