What it does

This tool creates a coverage report for QC purposes. By default, average coverage statistics are provided, taken from samtools flagstats. If specified, it can also create overviews per gene in the BED file, and sub-exon plots for failed exons.

BED format

The BED file containing targets of interest has very specific format requirements. You must use the following format:

Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1')
Column 2: Start Position
Column 3: End Position
Column 4: Target Name. Use : "GENE-NAME|Exon_number" : This is split on the pipe (or space) after 'GeneName' for correct grouping.Example: "CLIP2|Exon_4"
Column 5: Score : ignored, use '0'
Column 6: Strand: ignored,'+' or '-'

Note: The exons for the plots will be ordered in the same way as the exons in the BED file.

Input formats

BAM file for reads, BED file for targets.

Outputs

The output files are a PDF report and a tar.gz file with all the plots and output tables. The output tables are (tab seperated txt files):

Targets.Global.Coverage : Original BED file + following columns::

• Total coverage in target
• Bases in target with coverage
• Length of target
• Percent of target covered

Targets.Position.Coverage : Original BED file + following columns::

• Position in target region
• Coverage at position