| | The TSC read set (available from ftp.snp.cshl.org) were clipped using ssahaCLIP ( ftp://ftp.ensembl.org/pub/traces/homo_sapiens/clip/README-clip; reads also available here as ftp://ftp.ensembl.org/pub/traces/homo_sapiens/clip/cshl-human-wgs-*.clip.gz.) wh |
| | ich set a usable read length for each read. The reads were aligned using SsahaSNP to build 33 of NCBI the Reference Sequences. Quality values were not used for this genomic sequence. Where reads matched the genome more than once, the best quality match wa |
| | s used. 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. When both the |
| | Q>=23 threshold and the neighbourhood restrictions are met, the base then meets the Neighbourhood Quality Standard (NQS). If the (number of SNPs detected for a read)/(number of NQS aligned bases for that read) is determined to have a ratio > 15SNPs/1kb of |
| | sequence then all SNPs were discarded for that read alignment. |
