Submitter Method Handle: | CSHL-HAPMAP | Submitter Method ID: | CSHL-HUAA-200402 | Submitted method description: | |
| We aligned 2,783,661 human reads, individual A (see Venter JC, et al, The Sequence of the Human Genome, Science Feb 16 2001: 1304-1351), | | to build34 of the human genome, available at ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/, using ssahaSNP. The settings for ssahaSNP were | | such that the candidate SNP base in the read was at least Phred Q=23, that its neighbouring 5 bases on either side of the candidate SNP a | | ll had Phred quality values of >=15 and at least 9 of the 10 neighbours match. If the number of detected SNPs for the aligned segment of | | a read exceeded a rate of 15 SNPs per 1000 bases then that read alignment was ignored. If a read aligned to more than one place in the ge | | nome, then only the longest alignment with the fewest SNPs was reported. |
This method was used in the following submission:
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