| | The following method definition consists of one or more |
| | protocols used in The SNP Consortium project by the |
| | participating laboratory WUGSC. |
| | See the TSC website (http://snp.cshl.org/cgi-bin/protocol) |
| | for a complete list of TSC protocols. |
| | \\--------------------------------------- |
| | SNP production protocol TSCM0001 ( |
| | http://snp.cshl.org/cgi-bin/protocol?id=TSCM0001) |
| | Title: SNP discovery protocol GSC-SNP-protocol-1 |
| | Lab: Washington University Genome Sequencing Center |
| | Contact: [email protected] |
| | Description: |
| | LIBRARY: |
| | Small-insert plasmid (pZERO2) library representing 10 heterozygous individuals. |
| |
|
| | SEQUENCING:
|
| | Samples were sequenced using big-dye terminator chemistry, on ABI 3700 |
| | sequencers. |
| | \\--------------------------------------- |
| | SNP detection protocol TSCM0002 ( |
| | http://snp.cshl.org/cgi-bin/protocol?id=TSCM0002) |
| | Title: Custom clustering + Phrap multiple alignments + PolyBayes SNP detection |
| | Lab: Washington University Genome Sequencing Center |
| | Contact: [email protected] |
| | Description: |
| | SUMMARY: |
| | Sequences were clustered with custom scripts, using WU-BLAST for similarity |
| | searches. Sequences within clusters were multiply aligned with Phrap. |
| | The identification of likely paralogous (or repetitive) sequences within |
| | clusters and SNP detection was performed by an adaptation of the PolyBayes |
| | SNP analysis approach (and the corresponding computer implementation). |
| |
|
| | CLUSTERING: |
| | Full pair-wise comparison between all reads was performed with WU-BLAST. |
| | Clusters were created with a greedy method. |
| |
|
| | MULTIPLE ALIGNMENT: |
| | Cluster members were multiply aligned with Phrap. |
| |
|
| | PARALOG (OR REPEAT) FILTERING: |
| | A Bayesian statistical approach is used to determine if cluster members |
| | represent a unique genomic location (as opposed to multiple, duplicated |
| | regions) (An adaptation of the PolyBayes SNP analysis approach). |
| |
|
| | SNP DETECTION: |
| | A Bayesian statistical approach is used to determine if a slice of a |
| | multiple alignment is likely to be polymorphic (as opposed to monomorphic) |
| | given the base calls and base quality values of each sequence contributing to |
| | the site under examination (An adaptation of the PolyBayes SNP analysis |
| | approach). |
