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Common options

One of the advantages of the Bamformatics toolkit is that its individual programs accept a common set of options, for which default values can be set. This is valuable as it enables the bioinformatician to execute steps in a long workflow in a consistent manner. It also facilitates manual or exploratory execution of customized data processing on the command-line.

Setting default values

All the available common options and their associated default values can be accessed via the command

java -jar Bamformatics.jar defaults –-show

To change the default value for any of the options, use for example

java -jar Bamformatics.jar defaults --genome /path/to/genome.fa

To restore the hard-coded defaults, use

java -jar Bamformatics.jar defaults --reset

Meaning

Below is an synopsis of each of the options. In parenthesis are the programs that use the option.

genome - path to a reference genome (variants)

minallelic – a fraction between 0 and 1 - minimum proportion of alternative bases at a locus required to call a variant (variants)

minbasequal – ASCII character - minimum base quality value to considered a base in analysis (variants, tracks)

mindepth – non-negative integer - minimum number of reads with an alternative base at a locus required to call a variant (variants)

minfromstart - non-negative integer - number of the bases at 5prime end of read to exclude from analysis (variants, tracks)

minfromend – non-negative integer - number of the bases at 3prime end of read to exclude from analysis (variants, tracks)

minmapqual – non-negative integer - minimum mapping quality for a read to be included in analysis (variants, tracks)

minscore – non-negative value - minimum threshold score required to call a variant (variants)

strandbias – value between 0 and 1 - threshold p-value for a strand bias Fisher-test (variants)

trim – true/false - whether or not to exclude homo-polymer chains at read start/end (variants, tracks)

trimQB – true/false, whether or not to exclude bases with base-quality 'B' at read start/end (variants, tracks)