ayb-recal [-a description] [-m max-quality] -v [-w window-size] file1.sam file2.sam …

ayb-recal --help

ayb-recal --licence


ayb-recal is a utility to create calibration files for the AYB base caller from SAM alignment files. The alignment files should contain the MD optional tag; these are in the SAM output of many aligners but can be added to a BAM file (and hence to SAM) using samtools(1).


samtools fillmd aln.bam ref.fasta

ayb-recal reads from files specified and prints summary to stdout. If no files are specified on commandline, ayb-recal reads from stdin.

-a, --ayb description [default: display summary]

Output calibration table in a format usable by the AYB base-caller. The description is a free text field, that generally should be enclosed in quotes on the command-line. E.g. ayb-recal -a "Run: AYB00001. sample: NA19240"

-m, --maxqual max-quality [default: 60]

Maximum (integral) quality value to consider. Data is binned 0 to maxqual, according to quality value, to fit model to. If a quality value greater than is threshold is encountered, it is rounded down and a warning is issued.

-v, --variance

Weight linear fit by inverse variance of phred estimate rather than by number of observations (default). The variance is calculated using the Delta method.

-w, --window window-size [default: 3]

Window size around current base to use as context, which should be odd. The default is one base either side (window-size 3). A value of 0 means that the current base should not be taken into account either.

-h, --help

Display information about usage and exit.


Display licence terms and exit.


Output of ayb-recal is a header file to be compiled into AYB.


Written by Tim Massingham,



Copyright © 2010 European Bioinformatics Institute. Free use of this software is granted under the terms of the GNU General Public License (GPL). See the file COPYING in the ciftools distribution or for details.