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SeqSIMLA V2.9.1

The current version is 2.9.1 (SeqSIMLA2.9.1). We ported the Java code in version 1.0 to C++ in SeqSIMLA2. Speed is improved by implementing more efficient algorithms in the new version. Several new features are added in version 2.0, mostly for simulating quantitative traits.

Update(2017/08/31): Bug fixed. see change log
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SeqSIMLA V1

SeqSIMLA can simulate sequence data in families with multiple affected and unaffected siblings or unrelated case-control under different disease models.

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Reference Sequence Files

Sequence File Recombination File Frequency File
Asian chromosome 1 ASN_chr1.bed.gz ASN_chr1.rec ASN_chr1.freq
Asian 500kb on chrom 1: ASN_500k.bed.gz ASN_500k.rec ASN_500k.freq
African chromosome 1 AFR_chr1.bed.gz AFR_chr1.rec AFR_chr1.freq
African 500kb on chrom1 AFR_500k.bed.gz AFR_500k.rec AFR_500k.freq
European chromosome 1 EUR_chr1.bed.gz EUR_chr1.rec EUR_chr1.freq
European 500kb on chrom 1 EUR_500k.bed.gz EUR_500k.rec EUR_500k.freq
The reference sequence files were generated based on the 1000 Genomes Project sequence data for the Asian, African and European populations. For more details of generating the datasets, please refer to the SeqSIMLA2 paper (Chung et al. 2015 Genetic Epidemiology).

The sequence and recombination files can be used in SeqSIMLA2 to generate sequences with allele frequencies and LD structures similar to those in the selected population. The frequency files show minor allele frequencies for sites in the sequence files.

Note that the frequency files are not required for SeqSIMLA2, but they can be used to select disease sites before running SeqSIMLA2.

If you would like to know the variant info (such as SNP names and positions) in the reference sequence files, please refer to the legend file for chromosome 1 or 500kb on chrom 1.