Author: Pandya, Gagan A.; Holmes, Michael H.; Sunkara, Sirisha; Sparks, Andrew; Bai, Yun; Verratti, Kathleen; Saeed, Kelly; Venepally, Pratap; Jarrahi, Behnam; Fleischmann, Robert D.; Peterson, Scott N.
Title: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform Document date: 2007_11_15
ID: 16tii0ha_47
Snippet: The computational requirements of these filters are modest. We routinely run them on a 2.8 MHz Xeon Õ dualprocessor Linux workstation. A set of six F. tularensis chips representing one experiment can be processed in an The genome-adjusted results are calculated relative to the portions of the chip set that performed well with the DNA samples under consideration. The regions identified by our low-homology filter are excluded from the genome-adjus.....
Document: The computational requirements of these filters are modest. We routinely run them on a 2.8 MHz Xeon Õ dualprocessor Linux workstation. A set of six F. tularensis chips representing one experiment can be processed in an The genome-adjusted results are calculated relative to the portions of the chip set that performed well with the DNA samples under consideration. The regions identified by our low-homology filter are excluded from the genome-adjusted positions. The false-negative SNP counts represent the number of expected SNPs that were missing from the final, filtered SNP set. For SCHU S4, 7464 SNPs were expected, on the basis of in silico alignment of the LVS and SCHU S4 genome sequences. In the false-positive SNP rate calculation, the denominator is the number of genomeadjusted base positions that were not expected to be SNPs. In the false-negative SNP rate calculation, the denominator is the number of genome-adjusted positions that were expected to be SNPs.
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