Table 4.

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

SAMTools option	description	short symbol	long symbol	default
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