last-pair-probs1
Read alignments of paired dna reads to a genome, and do estimations
Usage
last-pair-probs [options]
interleaved-alignments
last-pair-probs [options]
alignments1
alignments2
Overview
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
Releases
7 releases since Debian 7 (Wheezy); the text changed 2 times.
--estdist since Debian 8 (Jessie);
--version since Debian 9 (Stretch);
-V since Debian 9 (Stretch);
-e since Debian 8 (Jessie).
--genome until Debian 7 (Wheezy);
-g until Debian 7 (Wheezy).