Table 4 SAMtools options recognised by the Bio::DB:Sam#mpileup method and the symbols used to invoke them

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