get_mismatch_genomic_pos_list: Get list of genomic positions with mismatches

In JakobPedersenLab/dreams: Deep Read-level Error Model for Sequencing data

Get list of genomic positions with mismatches

Description

This function computes the genomic positions of mismatches in sequencing reads based on the MD tag from BAM files. The MD tag describes how the read aligns to the reference genome, including mismatches. The function identifies these mismatches and computes their positions relative to the start of the alignment, aiding in variant calling and analysis of sequencing errors.

Usage

get_mismatch_genomic_pos_list(pos, MDtag)

Arguments

pos	Genomic position
MDtag	MD tag string from the BAM file that contains information about matches, mismatches, and deletions in the read alignment.

Value

A list of genomic positions where mismatches occur, corresponding to each MD tag provided.

JakobPedersenLab/dreams documentation built on Feb. 2, 2024, 3:14 p.m.