|
r
|
limit retrieval to a region
|
:r
|
:region
|
all positions
|
|
6
|
assume Illumina scaled quality scores
|
:six
|
:illumina_quals
|
FALSE
|
|
A
|
count anomalous read pairs scores
|
:A
|
:count_anomalous
|
FALSE
|
|
B
|
disable BAQ computation
|
:B
|
:no_baq
|
FALSE
|
|
C
|
parameter for adjusting mapQ
|
:C
|
:adjust_mapq
|
0
|
|
d
|
max per-BAM depth to avoid excessive memory usage
|
:d
|
:max_per_bam_depth
|
250
|
|
E
|
extended BAQ for higher sensitivity but lower specificity
|
:E
|
:extended_baq
|
FALSE
|
|
G
|
exclude read groups listed in FILE
|
:G
|
:exclude_reads_file
|
FALSE
|
|
l
|
list of positions (chr pos) or regions (BED)
|
:l
|
:list_of_positions
|
FALSE
|
|
M
|
cap mapping quality at value
|
:M
|
:mapping_quality_cap
|
60
|
|
R
|
ignore RG tags
|
:R
|
:ignore_rg
|
FALSE
|
|
q
|
skip alignments with mapping quality smaller than value
|
:q
|
:min_mapping_quality
|
0
|
|
Q
|
skip bases with base quality smaller than value
|
:Q
|
:imin_base_quality
|
13
|
