grit coverage
Calculate coverage of A intervals by B intervals.
Usage
grit coverage [OPTIONS] -a <FILE_A> -b <FILE_B>
Options
| Option | Description |
|---|---|
-a, --file-a <FILE> | Input BED file A (regions) |
-b, --file-b <FILE> | Input BED file B (reads/features) |
--hist | Report a histogram of coverage |
-d, --per-base | Report depth at each position |
--mean | Report mean depth |
--assume-sorted | Skip sorted validation |
-g, --genome <FILE> | Genome file for validation |
Examples
Basic coverage
# Calculate coverage of genes by reads
grit coverage -a genes.bed -b reads.bed > coverage.bed
# With sorted input (faster)
grit coverage -a genes.bed -b reads.bed --assume-sorted
Coverage histogram
# Generate coverage histogram
grit coverage -a regions.bed -b reads.bed --hist > histogram.txt
Per-base depth
# Report depth at each position
grit coverage -a genes.bed -b reads.bed -d > per_base.bed
Mean coverage
# Report mean coverage depth
grit coverage -a genes.bed -b reads.bed --mean > mean_coverage.bed
Output
Default output (7 columns):
chr1 100 200 3 75 100 0.7500000
| Column | Description |
|---|---|
| 1-3 | Chromosome, start, end (from A) |
| 4 | Number of B intervals overlapping |
| 5 | Number of bases covered |
| 6 | Length of A interval |
| 7 | Fraction of A covered |
With –hist:
chr1 100 200 0 25
chr1 100 200 1 50
chr1 100 200 2 25
all 0 100 25
all 1 100 50
all 2 100 25
With -d (per-base):
chr1 100 2
chr1 101 2
chr1 102 3
...
Use Cases
RNA-seq gene coverage
grit coverage -a genes.bed -b aligned_reads.bed --assume-sorted > gene_coverage.bed
ChIP-seq peak coverage
grit coverage -a peaks.bed -b reads.bed --mean > peak_depths.bed
Exome coverage analysis
grit coverage -a exome_targets.bed -b wes_reads.bed --hist > coverage_hist.txt
Performance
# Fastest with sorted input
grit coverage -a sorted_regions.bed -b sorted_reads.bed --assume-sorted