Aligner Options

aln-min-score

(signed) Minimum alignment score to report; baseline for MAPQ.

When using local alignments (global = 0), aln-min-score is computed by the host software as "22 * match-score".

When using global alignments (global = 1), aln-min-score is set to -1000000.

Host software computation may be overridden by setting aln-min-score in configuration file.

--Aligner.aln-min-score

dedup-min-qual

Minimum base quality for calculating read quality metric for deduplication.

--Aligner.dedup-min-qual

en-alt-hap-aln

Allows chimeric alignments to be output, as supplementary.

--Aligner.en-alt-hap-aln

en-chimeric-aln

Allows chimeric alignments to be output, as supplementary.

--Aligner.en-chimeric-aln

gap-ext-pen

Score penalty for gap extension.

--Aligner.gap-ext-pen

gap-open-pen

Score penalty for opening a gap (insertion or deletion).

gap-open-pen

global

If alignment is global (Needleman-Wunsch) rather than local (Smith-Waterman).

--Aligner.global

hard-clips

Flags for hard clipping: [0] primary, [1] supplementary, [2] secondary.

--Aligner.hard-clips

map-orientations

Constrain orientations to accept forward-only, reverse-complement only, or any alignments.

--Aligner.map-orientations

mapq-max

Ceiling on reported MAPQ.

--Aligner.mapq-max

mapq-strict-js

Specific to RNA. When set to 0, a higher MAPQ value is returned, expressing confidence that the alignment is at least partially correct. When set to 1, a lower MAPQ value is returned, expressing the splice junction ambiguity.

--mapq-strict-js

match-n-score

(signed) Score increment for matching a reference 'N' nucleotide IUB code.

--Aligner.match-n-score

match-score

Score increment for matching reference nucleotide.

--Aligner.match-score

min-score-coeff

Adjustment to aln-min-score per read base.

--Aligner. min-score-coeff

mismatch-pen

Score penalty for a mismatch.

--Aligner.mismatch-pen

no-unclip-score

When no-unclip-score is set to 1, any unclipped bonus (unclip-score) contributing to an alignment is removed from the alignment score before further processing.

--Aligner.no-unclip-score

no-unpaired

If only properly paired alignments should be reported for paired reads.

--Aligner. no-unpaired

pe-max-penalty

Maximum pairing score penalty, for unpaired or distant ends.

--Aligner.pe-max-penalty

pe-orientation

Expected paired-end orientation: 0=FR, 1=RF, 2=FF.

--Aligner.pe-orientation

rescue-sigmas

Deviations from the mean read length used for rescue scan radius. Default is 2.5.

--Aligner.rescue-sigmas

sec-aligns

Maximum secondary (suboptimal) alignments to report per read.

--Aligner.sec-aligns

sec-aligns-hard

Set to force unmapped when not all secondary alignments can be output.

--Aligner.sec-aligns-hard

sec-phred-delta

Only secondary alignments with likelihood within this Phred of the primary are reported.

--Aligner.sec-phred-delta

sec-score-delta

Secondary aligns allowed with pair score no more than this far below primary.

--Aligner. sec-score-delta

supp-aligns

Maximum supplementary (chimeric) alignments to report per read.

--Aligner.supp-aligns

supp-as-sec

If supplementary alignments should be reported with secondary flag.

--Aligner.supp-as-sec

supp-min-score-adj

Amount to increase minimum alignment score for supplementary alignments. This score is computed by host software as "8 * match-score" for DNA, and is default 0 for RNA.

--Aligner. supp-min-score-adj

unclip-score

Score bonus for reaching each edge of the read.

--Aligner.unclip-score

pe-stat-mean-insert

Average template length.

pe-stat-mean-read-len

Average read length.

pe-stat-quartiles-insert

A comma-delimited trio of numbers specifying 25^th, 50^th, and 75^th percentile template lengths.