pbr

drunk on perbase pileups and lua expressions.

Usage

Basic Usage

pbr <BAM_FILE> -f <FASTA_FILE> -t <THREADS> --mate-fix --max-depth <MAX_DEPTH> -k <FLANKING>

Examples

Single Base Reference (-k 0)

pbr test/simple_test.bam -f test/simple_test.fa -t 4 --mate-fix --max-depth 500000 -k 0

Multi-Base Reference Window (-k 1)

pbr test/simple_test.bam -f test/simple_test.fa -t 4 --mate-fix --max-depth 500000 -k 1

Filter rows where the reference base is 'A':

pbr test/simple_test.bam -f test/simple_test.fa -t 4 --mate-fix --max-depth 500000 -k 0 --pile-expression "return pile.ref_base == 'A'"

Filter rows where the reference window is 'AAG':

pbr test/simple_test.bam -f test/simple_test.fa -t 4 --mate-fix --max-depth 500000 -k 1 --pile-expression "return pile.ref_base == 'AAG'"

Filter reads with a specific tag, e.g., RG:Z:test:

pbr test/simple_test.bam -f test/simple_test.fa -t 4 --mate-fix --max-depth 500000 -k 0 --pile-expression "return read:tag('RG') == 'test'"

Lua Filtering

The --expression (-e) option allows you to filter reads using Lua expressions. The read object exposes the following fields:

• qname: Query name
• ....

The --pile-expression (-p) option allows you to filter rows using Lua expressions. The pile object exposes the following fields:

• depth: Read depth
• a, c, g, t, n: Counts of each base
• ins, del, ref_skip, fail: Counts of insertions, deletions, reference skips, and failed reads
• pos: 0-based position
• ref_base: Reference base or window (e.g., 'A' for -k 0, 'AAG' for -k 1)

Output

The output is a tab-separated file with the following columns:

• #chrom: Chromosome name
• pos0: 0-based position
• ref_base: Reference base or window (e.g., 'A' for -k 0, 'AAG' for -k 1)
• depth: Read depth
• a, c, g, t, n: Counts of each base