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Method Detail
Submitter Method Handle: TSC-CSHL
Submitter Method ID: TSC-CSHL-30
Submitted method description:
The following method definition consists of one or more
protocols used in The SNP Consortium project by the
participating laboratory CSHL.
See the TSC website (http://snp.cshl.org/cgi-bin/protocol)
for a complete list of TSC protocols.
\\---------------------------------------
SNP detection protocol TSCM0030 (
http://snp.cshl.org/cgi-bin/protocol?id=TSCM0030)
Title: SNP detection using ssahaSNP program for WUGSC trace files
Lab: Cold Spring Harbor Laboratory
Contact: kakol@cshl.org
Description:
Reads were clipped by removing all positions from each end up to the
first position of quality at least 20. The reads were aligned using
SsahaSNP to available finished and unfinished (with quality values)
public human genomic sequence which is available via anonymous ftp at
snp.cshl.org in the files pub/SNP/gbfinished* and pub/SNP/nr*. All
reads which aligned to genomic sequence were assembled with the
matching region of genomic sequence (Q was set to 40 for finished
genomic sequence). High quality base discrepancies (Q>=23) were
identified as candidate SNPs. Further restrictions on the candidate
SNPs were that its neighbouring 5 bases all had Phred quality values of
>=15 and at least 9 of the 10 neighbours match. If the number of
detected SNPs in one clique was greater than 4 then all SNPs were
discarded for that clique.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
TSC-CSHL Assay TSC-CSHL-30_101052517 96
TSC-CSHL Assay TSC-CSHL-30_101091916 100
TSC-CSHL Assay TSC-CSHL-Sep-19-2002-SNP_SUBMISSION-30 107

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