Scoring options:¶

-A INT

score for a sequence match, which scales options -TdBOELU unless overridden [1]

-B INT

penalty for a mismatch [4]

-O INT[,INT]

gap open penalties for deletions and insertions [6,6]

-E INT[,INT]

gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]

-L INT[,INT]

penalty for 5'- and 3'-end clipping [5,5]

-U INT

penalty for an unpaired read pair [17]

Input/output options:¶

-p

smart pairing (ignoring in2.fq)

-R STR

read group header line such as '@RG\tID:foo\tSM:bar' [null]

-H STR/FILE

insert STR to header if it starts with @; or insert lines in FILE [null]

-j

treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)

-5

for split alignment, take the alignment with the smallest coordinate as primary

-q

don't modify mapQ of supplementary alignments

-K INT

process INT input bases in each batch regardless of nThreads (for reproducibility) []

-v INT

verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]

-T INT

minimum score to output [30]

-h INT[,INT]

if there are <INT hits with score >80% of the max score, output all in XA [5,200]

-a

output all alignments for SE or unpaired PE

-C

append FASTA/FASTQ comment to SAM output

-V

output the reference FASTA header in the XR tag

-Y

use soft clipping for supplementary alignments

-M

mark shorter split hits as secondary

-I FLOAT[,FLOAT[,INT[,INT]]]

specify the mean, standard deviation (10% of the mean if absent), max (4 sigma from the mean if absent) and min of the insert size distribution. FR orientation only. [inferred]

Note: Please read the man page for detailed description of the command line and options.