NAME¶

last-pair-probs.py - Read alignments of paired DNA reads to a genome

DESCRIPTION¶

Usage:¶

last-pair-probs.py --help last-pair-probs.py [options] alignments1 alignments2

Read alignments of paired DNA reads to a genome, and estimate the probability that each alignment represents the genomic source of the read.

OPTIONS¶

-h, --help

show this help message and exit

-r, --rna

specifies that the reads are from potentially-spliced RNA

-m M, --mismap=M

don't write alignment pairs with mismap probability > M (default: 0.01)

-f BP, --fraglen=BP

mean fragment length in bp

-s BP, --sdev=BP

standard deviation of fragment length

-g BP, --genome=BP

haploid genome size in bp

-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)