Reference Haplotype Files
For running FAST with summary data (i.e, option --mode summary), you will need the reference haplotypes from an appropriate population. For every chromosome, you will need the following two files:
Haplotye file (option --hap-file): This tab-delimited file specifies the reference haplotypes for computing LD on the fly.
Haplotye index file (option --pos-file): This tab-delimited file specifies the reference haplotypes start byte positions for computing LD on the fly.
For more details see Input File Format
We provide the pre-computed haplotype files and their corresponding index files (for input with options --hap-file, --pos-file) from 1000 Genomes Project (released on May 2012) for the following commonly used reference populations.
Please use the correct reference panel with same ethnicity as the study sample for gene-based analysis.
Do not forget the option "--compute-ld".
We plan to add more to these in near future. If you need any specific population for running FAST, please let us know, we will prepare the data for you.
These files (one for each chromosome) maintain a pre-computed list of problematic SNPs that are mapped to multiple loci and will be skipped during analysis with summary data. If you find any specific SNP you want to omit from your analysis, include the snp id (rs no) in the file for the appropriate chromosome.