Genomic Region Coverage

Requirements

This script requires:

• samtools
• python libraries:
  • matplotlib
  • seaborn

Usage

python get_exon_coverage.py [-h] --output_root OUTPUT_ROOT --bam_input BAM_INPUT --ref_gene_file REF_GENE_FILE
                            --gene_exon_list_file GENE_EXON_LIST_FILE

• --output_root OUTPUT_ROOT Root for output report files and plots

• --bam_input BAM_INPUT Path to the BAM input file. BAI file is assumed to exist and be in the standard location.

• --ref_gene_file REF_GENE_FILE Path to the refGene.txt file containing gene and exon information, downloadable from here: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/

• --gene_exon_list_file GENE_EXON_LIST_FILE Path to the gene exon list file. This is a file with each gene of interest on each line.

Output

Statistics are reported for the following metrics:

• min_per_nucleotide_depth: Minimum per-nucleotide read depth per exon
• mean_per_nucleotide_depth: Mean per-nucleotide read depth per exon
• median_per_nucleotide_depth: Median per-nucleotide read depth per exon
• max_per_nucleotide_depth: Maximum per-nucleotide read depth per exon
• bq30_min_per_nucleotide_depth: Minimum per-nucleotide read depth for bases with quality >30 per exon
• bq30_mean_per_nucleotide_depth: Mean per-nucleotide read depth for bases with quality >30 per exon
• bq30_median_per_nucleotide_depth: Median per-nucleotide read depth for bases with quality >30 per exon
• bq30_max_per_nucleotide_depth: Maximum per-nucleotide read depth for bases with quality >30 per exon
• mq20_min_per_nucleotide_depth: Minimum per-nucleotide read depth for reads with mapping quality >20 per exon
• mq20_mean_per_nucleotide_depth: Mean per-nucleotide read depth for reads with mapping quality >20 per exon
• mq20_median_per_nucleotide_depth: Median per-nucleotide read depth for reads with mapping quality >20 per exon
• mq20_max_per_nucleotide_depth: Maximum per-nucleotide read depth for reads with mapping quality >20 per exon
• total_reads_processed: Total reads per exon
• count_reads_unaligned: Count of reads unaligned per exon
• count_reads_not_primary_alignment: Count of reads not primary alignment per exon
• count_reads_mate_unaligned: Count of reads with mate unaligned per exon
• count_reads_mate_on_other_chr: Count of reads with mate on other chromosome per exon
• count_reads_mate_gt_10kb_away: Count of reads with mate >10kb away per exon
• count_reads_soft_clipped: Count of soft clipped reads per exon
• count_reads_hard_clipped: Count of hard clipped reads per exon
• count_reads_fw_strand: Count of reads on forward strand per exon
• pct_reads_unaligned: Percent of unaligned reads per exon
• pct_reads_not_primary_alignment: Percent of not primary alignment reads per exon
• pct_reads_mate_unaligned: Percent of reads with mate unaligned per exon
• pct_reads_mate_on_other_chr: Percent of reads with mate on another chromosome per exon
• pct_reads_mate_gt_10kb_away: Percent of reads with mate >10kb away per exon
• pct_reads_soft_clipped: Percent of soft clipped reads per exon
• pct_reads_hard_clipped: Percent of hard clipped reads per exon
• pct_reads_fw_strand: Percent of reads on forward strand per exon
• per_base_unaligned: Number of unaligned reads per base per exon
• per_base_not_primary_alignment: Number of not primary alignment reads per base per exon
• per_base_mate_unaligned: Number of reads with mate unaligned per base per exon
• per_base_mate_on_other_chr: Number of reads with mate on another chromosome per base per exon
• per_base_mate_gt_10kb_away: Number of reads with mate >10kb away per base per exon
• per_base_soft_clipped: Number of soft clipped reads per base per exon
• per_base_hard_clipped: Number of hard clipped reads per base per exon