Distinguishing heterozygous sites from systematic errors
SysCall is a logistic regression based classifier.
Given a list of candidate heterozygous genomic locations and a sam file of sequenced reads SysCall classifies each genomic location as either a heterozygous site or a systematic error and outputs according lists, along with the assigned posterior probabilities.
The submitted manuscript describing SysCall can be found here and the lists of systematic errors reported in the paper are here .
The slides from a talk on SysCall given at the 2011 CSHL Meeting on The Biology of Genomes can be found here.
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If you use SysCall, please cite
F Meacham, D Boffelli, J Dhahbi, DI Martin, M Singer and L Pachter: Identification and correction of systematic error in high-throughput sequence data, in press.