fillGapsWithBam: This function will take both assembled haplotypes and will...

In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

This function will take both assembled haplotypes and will try to fill gaps at positions where only one allele is phased Such position have to be heterozygous so the alternative allele at this position can be reliably distinguished

Description

This function will take both assembled haplotypes and will try to fill gaps at positions where only one allele is phased Such position have to be heterozygous so the alternative allele at this position can be reliably distinguished

Usage

fillGapsWithBam(
  data.object,
  merged.bam,
  min.mapq = 10,
  min.baseq = 30,
  translateBases = FALSE,
  chromosome = NULL,
  chunkSize = 1e+07,
  filterAltAlign = TRUE
)

Arguments

data.object	...
merged.bam	...
min.mapq	Minimum mapping quality when importing from BAM files.
min.baseq	Minimum base quality to consider a base for phasing.
translateBases	translates integer coded bases (1,2,3,4) into letters (A,C,G,T)
chromosome	If only a subset of the chromosomes should be processed, specify them here.
chunkSize	...

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on April 7, 2024, 7:13 p.m.