inst/extdata/prep_input.md

In Manuelaio/uncoverappLib: Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Preparation input file

In this section users can prepare bed file required for clinical assessment of low depth of coverage genomic regions. The resulting unCOVERApp input file is a BED file (tab-separated) containing a minimum of five columns, chromosome, start and end position, depth of coverage (DoC) and nucleotide counts for each genomic position of target genes for as many samples as many BAM files are listed in the ".list" file.

The processing time depends on the dimension size of bam files and the number of genes to investigate. If many genes need to be analyzed, we recommend using buildInput function before to launch the App and to load the output file in Coverage Analysis page

Documentation

To prepare input file and investigate coverage annotation the following input parameters must be specified in the sidebar of the preprocessing section:

• Genome: choose reference genome (hg19 or hg38)

• Chromosome Notation : chromosome notation BAM. IN bam file number refers to chromosome notation as 1, 2, ..., X,.M, chr refers to chr1, chr2, ... chrX, chrM.

• Load input file : loading txt file containing HGNC gene name(s) (one per row) or a target bed

• Choose the type of your input file : selecting the type of input file

• Load bam file(s) list : loading path to file with ".list" extension containing absolute paths to BAM files (one per row)

• minimum mapping quality (MAPQ): default value 1

• minimum base quality (QUAL) : default value 1

Users can download Statistical_Summary report to obtain a coverage metrics per genes (List of genes name) or per amplicons (Target Bed) according to uploaded input file. The report summarizes following information: mean, median, number of positions under 20x and percentage of position above 20x

Manuelaio/uncoverappLib documentation built on Feb. 16, 2023, 12:52 a.m.