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Method Detail
Submitter Method Handle: ABI
Submitter Method ID: XPLORE
Submitted method description:
We have developed SNP Xplore pipeline to mine single nucleotide substitutions, short deletion and insertion polymorphisms from Celera whole-genome shotgun assembly (WGA) (1, 2). The pipeline includes three major processes:
1. Identify the potential nucleotide variants from the WGA2 alignment, which includes all Celera reads and public BACtigs. All fragments imported for the Assembler have been cleaned and trimmed by the assembly process (1). The potential nucleotide v
ariants need to pass the sequence quality value (QV), neighbor quality value (NQV) and the heterozygosity check. The default QV value is > 23 for the polymorphic base and >21 for the minimal neighbor QV (4 bps). For indel variations, which only the neighb
or QV are available, the default minimal NQV should be >23. In addition to this general simple QV rule, Xplore implemented our plurality rule. This rule scavenges the SNPs with marginal level of QV. For the deep covered minor alleles, the QV threshold is
adjusted lower. Every supported minor allele will decrease the threshold, but the minimal QV cutoff is not below 16.
2. Measure the SNP features (3). Each potential SNP was gone through our quality assessment metric for getting a set of assessment values, including neighbor variant density (NB20), Binomial Probability P(n,k), fragment edge measure (EM), SNP type,
Phred quality value, neighbor quality value, neighbor nucleotide composition, pairwise dissimilarity rate, and donor and allele frequency.
3. Selection process. Based on the quality assessment metric, the SNP were selected based on the composite consideration of each individual criterion. For high quality SNPs in this dump, we selected the composite index: matrixN. This matrix has been
tested for giving the highest ratio of validated vs non validated SNPs from our in house resequence project.
Reference -
(1) Venter, Craig; et al. Science vol. 291, no.5507, p. 1304 ? 1351, 2001
(2) Istrail, Sorin; et al. PNAS vol. 101, no. 7, p. 1916 -1921, 2004
(3) Gu, Zhiping; Nathan Edwards, Cai, Shuang; Levitsky, Alexander; Fosler, Carl; Chiang, Chia-Chien; Wan, Chunhua; Ingber, Daniel; Li, Peter, Mining quality SNPs from Whole Genome Shotgun Assembly, in preparation

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
ABI Assay xplore_hum_chrY_1 125
ABI Assay xplore_hum_chr10_1 125
ABI Assay xplore_hum_chr11_1 125
ABI Assay xplore_hum_chr12_1 125
ABI Assay xplore_hum_chr10_2 125
ABI Assay xplore_hum_chr1_2 125
ABI Assay xplore_hum_chr11_2 125
ABI Assay xplore_hum_chr12_2 125
ABI Assay xplore_hum_chr13_2 125
ABI Assay xplore_hum_chr14_2 125
ABI Assay xplore_hum_chr15_2 125
ABI Assay xplore_hum_chr16_2 125
ABI Assay xplore_hum_chr17_2 125
ABI Assay xplore_hum_chr18_2 125
ABI Assay xplore_hum_chr19_2 125
ABI Assay xplore_hum_chr20_2 125
ABI Assay xplore_hum_chr21_2 125
ABI Assay xplore_hum_chr22_2 125
ABI Assay xplore_hum_chr2_2 125
ABI Assay xplore_hum_chr3_2 125
ABI Assay xplore_hum_chr4_2 125
ABI Assay xplore_hum_chr5_2 125
ABI Assay xplore_hum_chr6_2 125
ABI Assay xplore_hum_chr7_2 125
ABI Assay xplore_hum_chr8_2 125
ABI Assay xplore_hum_chr9_2 125
ABI Assay xplore_hum_chr13_1 125
ABI Assay xplore_hum_chrU_2 125
ABI Assay xplore_hum_chrU_1 125
ABI Assay xplore_hum_chrX_1 125
ABI Assay xplore_hum_chr14_1 125
ABI Assay xplore_hum_chrX_2 125
ABI Assay xplore_hum_chr15_1 125
ABI Assay xplore_hum_chr9_1 125
ABI Assay xplore_hum_chr16_1 125
ABI Assay xplore_hum_chr1_1 125
ABI Assay xplore_hum_chr17_1 125
ABI Assay xplore_hum_chrY_2 125
ABI Assay xplore_hum_chr18_1 125
ABI Assay xplore_hum_chr2_1 125
ABI Assay xplore_hum_chr19_1 125
ABI Assay xplore_hum_chr20_1 125
ABI Assay xplore_hum_chr21_1 125
ABI Assay xplore_hum_chr22_1 125
ABI Assay xplore_hum_chr3_1 125
ABI Assay xplore_hum_chr4_1 125
ABI Assay xplore_hum_chr5_1 125
ABI Assay xplore_hum_chr6_1 125
ABI Assay xplore_hum_chr7_1 125
ABI Assay xplore_hum_chr8_1 125
ABI Assay xplore_hum_chr10_1_rev 125
ABI Assay xplore_hum_chr10_2_rev 125
ABI Assay xplore_hum_chr11_1_rev 125
ABI Assay xplore_hum_chr11_2_rev 125
ABI Assay xplore_hum_chr12_1_rev 125
ABI Assay xplore_hum_chr12_2_rev 125
ABI Assay xplore_hum_chr13_1_rev 125
ABI Assay xplore_hum_chr13_2_rev 125
ABI Assay xplore_hum_chr14_1_rev 125
ABI Assay xplore_hum_chr14_2_rev 125
ABI Assay xplore_hum_chr15_1_rev 125
ABI Assay xplore_hum_chr15_2_rev 125
ABI Assay xplore_hum_chr16_1_rev 125
ABI Assay xplore_hum_chr16_2_rev 125
ABI Assay xplore_hum_chr17_1_rev 125
ABI Assay xplore_hum_chr17_2_rev 125
ABI Assay xplore_hum_chr18_1_rev 125
ABI Assay xplore_hum_chr18_2_rev 125
ABI Assay xplore_hum_chr19_1_rev 125
ABI Assay xplore_hum_chr19_2_rev 125
ABI Assay xplore_hum_chr1_1_rev 125
ABI Assay xplore_hum_chr1_2_rev 125
ABI Assay xplore_hum_chr20_1_rev 125
ABI Assay xplore_hum_chr20_2_rev 125
ABI Assay xplore_hum_chr21_1_rev 125
ABI Assay xplore_hum_chr21_2_rev 125
ABI Assay xplore_hum_chr22_1_rev 125
ABI Assay xplore_hum_chr22_2_rev 125
ABI Assay xplore_hum_chr2_1_rev 125
ABI Assay xplore_hum_chr2_2_rev 125
ABI Assay xplore_hum_chr3_1_rev 125
ABI Assay xplore_hum_chr3_2_rev 125
ABI Assay xplore_hum_chr4_1_rev 125
ABI Assay xplore_hum_chr4_2_rev 125
ABI Assay xplore_hum_chr5_1_rev 125
ABI Assay xplore_hum_chr5_2_rev 125
ABI Assay xplore_hum_chr6_1_rev 125
ABI Assay xplore_hum_chr6_2_rev 125
ABI Assay xplore_hum_chr7_1_rev 125
ABI Assay xplore_hum_chr7_2_rev 125
ABI Assay xplore_hum_chr8_1_rev 125
ABI Assay xplore_hum_chr8_2_rev 125
ABI Assay xplore_hum_chr9_1_rev 125
ABI Assay xplore_hum_chr9_2_rev 125
ABI Assay xplore_hum_chrU_2_rev 125
ABI Assay xplore_hum_chrX_2_rev 125
ABI Assay xplore_hum_chr4_2.2 125
ABI Assay xplore_hum_chr10_2.2 125