-
BWA
COMMANDS AND OPTIONS
index
bwa index
[-p prefix] [-a algoType] [-c] <>
Index database sequences in the FASTA
format.
OPTIONS:
-c
Build
color-space
index.
The
input
fast
should
be
in
nucleotide
space.
-p STR
P
refix of the
output database [same as db filename]
-a STR
A
lgorithm for constructing
BWT index. Available options are:
is
IS
linear-time
algorithm
for
constructing
suffix
array.
It
requires
5.37N
memory
where
N
is
the
size
of
the
database.
IS
is
moderately
fast,
but
does
not
work
with
database larger than 2GB. IS is the
default algorithm due
to
its
simplicity.
The
current
codes
for
IS
algorithm
are
reimplemented by Yuta Mori.
b
Algorithm
implemented
in
BWT-SW.
This
method
works
wt
with the whole human
genome, but it does not work with
sw
database smaller than 10MB
and it is usually slower than
IS.
aln
bwa aln [-n maxDiff] [-o maxGapO] [-e
maxGapE] [-d nDelTail]
[-i
nIndelEnd]
[-k
maxSeedDiff]
[-l
seedLen]
[-t
nThrds]
[-cRN]
[-M misMsc] [-O gapOsc] [-E gapEsc] [-q
trimQual] <>
<> > <>
Find
the
SA
coordinates
of
the
input
reads.
Maximum
maxSeedDiff
differences
are
allowed in
the
first
seedLen
subsequence
and
maximum
maxDiff differences
are allowed in the whole sequence.
OPTIONS:
-n
Maximum
edit
distance
if
the
value
is
INT,
or
the
fraction
of
NUM
missing alignments given 2% uniform
base error rate if FLOAT. In
the
latter
case,
the
maximum
edit
distance
is
automatically
chosen for
different read lengths. [0.04]
-o INT
Maximum number of
gap opens [1]
-e INT
Maximum
number
of
gap
extensions,
-1
for
k-difference
mode
(disallowing long gaps)
[-1]
-d INT
Disallow a long deletion within INT bp
towards the 3’
-end [16]
-i INT
Disallow
an indel within INT bp towards the ends [5]
-l INT
Take the first INT subsequence as seed.
If INT is larger than the
query
sequence,
seeding
will
be
disabled.
For
long
reads,
this
option is typically
ranged from 25 to 35 for ‘
-
k
2’. [inf]
-k INT
Maximum edit distance in the seed [2]
-t INT
Number
of threads (multi-threading mode) [1]
-M
Mismatch penalty. BWA
will not search for suboptimal hits with
INT
a score
lower than (bestScore-misMsc). [3]
-O
Gap open penalty [11]
INT
-E INT
Gap extension
penalty [4]
-R INT
Proceed with suboptimal alignments if
there are no more than
INT
equally
best
hits.
This
option
only
affects
paired-end
mapping.
Increasing this threshold helps to improve the
pairing
accuracy at the cost of speed,
especially for short reads (~32bp).
-c
-N
Reverse
query
but
not
complement
it,
which
is
required
for
alignment in the color
space.
Disable
iterative
search.
All
hits
with
no
more
than
maxDiff
differences
will
be
found.
This
mode
is
much
slower
than
the
default.
-q INT
Parameter
for
read
trimming.
BWA
trims
a
read
down
to
argmax_x{sum_{i=x+1}^l(INT-q_i)}
if
q_l
where
l
is
the
original read length. [0]
samse
bwa
samse
[-n
maxOcc]
<>
<>
<>
>
<>
Generate alignments in the SAM format
given single-end reads. Repetitive
hits
will be randomly chosen.