eba -- Estimates Base Accuracy in an SCF or ZTR file
eba [trace_file]
Eba will calculate numerical estimates of base accuracy for each
base in an SCF or ZTR file. The figures calculated should not be considered as
reliable and better values can be obtained from phred or ATQA.
The method employed by eba to estimate the base accuracies performs the following calculation for each base. Calculate the area under the peaks for each base type. Divide the area under the called base by the largest area under the other three bases. From the 2002 release these values are normalised to the phred scale (this was achieved by comaring the original eba values and phred values for 4.6 million base calls of Sanger Centre data).
With no filename as an argument eba reads from standard input and writes to standard output. This enables eba to be used as a filter, or to estimate base accuracies for unwritable files. If a file is specified on the command line then the accuracy figures will be written to this file.
To write base accuracy figures to an SCF file named e04f10.s1SCF.
eba e04f10.s1SCF
To write base accuracy figures on the original eba scale to an SCF file
named e04f10.s1SCF.
eba -old_scale e04f10.s1SCF
To write base accuracy figures to a ZTR file named e04f10.s1.ztr
in another users directory, and to store the updated file in the
current directory:
eba < ~user/e04f10.s1.ztr > e04f10.s1.ztr
See section scf(4).