last-pair-probs(1) Read alignments of paired DNA reads to a genome, and do estimations

SYNOPSIS

last-pair-probs/ [options] interleaved-alignments

last-pair-probs/ [options] alignments1 alignments2

DESCRIPTION

Read alignments of paired DNA reads to a genome, and: (1) estimate the distribution of distances between paired reads, (2) estimate the probability that each alignment represents the genomic source of the read.

OPTIONS

-h, --help
show this help message and exit
-r, --rna
assume the reads are from potentially-spliced RNA
-e, --estdist
just estimate the distribution of distances
-m M, --mismap=,M/
don't write alignments with mismap probability > M (default: 0.01)
-f BP, --fraglen=,BP/
mean distance in bp
-s BP, --sdev=,BP/
standard deviation of distance
-d PROB, --disjoint=,PROB/
prior probability of disjoint mapping (default: 0.02 if -r, else 0.01)
-c CHROM, --circular=,CHROM/
specifies that chromosome CHROM is circular (default: chrM)
-V, --version
show program's version number and exit