| 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. |