pbr

drunk on perbase pileups and lua expressions.

An example use is in calculating mutation rates. Variant callers have filters such as these that affect the number of mutations called; we also want to scale the denominator in similar way so we can compare rates across samples.

Expression

The following attributes are available on the read object in lua expressions:

``` mapping_quality flags # integer. must use bit32 lua module (builtin here) to do operations tid start stop

where in the current read is the pileup given by qpos with convenience of distancefrom[left/right]_end

qpos distancefrom5prime distancefrom3prime insertsize qname bq # basequality at current site length # length of the read sequence sequence nproportion5prime(bases:number) nproportion3prime(bases:number) indelcount softclips3prime softclips5_prime tag(name: string) ```

An example expression could be:

lua -- high mapping-q and base-quality for this column read.mapping_quality > 10 and read.bq > 20 \ -- and not within 10 bases of left end or right end and read.distance_from_5prime > 10 and read.distance_from_3prime > 10 \ -- and exclude read if unmapped, not primary, qc_fail, or duplicate. and bit32.band(read.flags, bit32.bor(4, 256, 512, 1024)) == 0 \ -- and exclude read if it has more than 5% N's in the sequence and string_count(read.sequence, 'N') < 0.05 * read.length

this runs as:

pbr $bam "return $expression" > out.pileup

where the $expression argument is the lua expression.

• Note that we can use, e.g. print(read.qname, read.flags); return $expression) to help with debugging.
• Note that the expression must contain 'return'

Usage

``` pileups filtered with lua expressions

Usage: pbr [OPTIONS]

Arguments: Path to the bamfile Lua expression to evaluate

Options: -t, --threads Number of threads to use [default: 2] -m, --max-depth maximum depth in the pileup [default: 100000] -b, --bedfile optional path to the BED of include regions -f, --fasta optional path to the reference fasta file -e, --exclude optional path to BED of exclude regions --mate-fix adjust depth to not double count overlapping mates -p, --pile-expression optional expression required for the pileup -h, --help Print help -V, --version Print version ```

PileExpression

Note that the pile-expression is also a lua expression; it is applied to the Pileup (column) rather than to the reads. The available attributes on the pile object are:

depth,a,c,g,t,n,fail,ins,del,ref_skip

An example --pile-expression would look like:

return pile.n / pile.depth < 0.05

To require that fewer than 5% of the reads in the pile are 'N'. Positions that do not pass this expression will not be printed.