I am a complete novice to haplotype analysis and I spent days to search for a tutorial or any guidance. No luck.
I have 400 subjects ( 200 CTRLs and 200 Cases) genotyped on an illumina platform.
I used my data in PLINK files to phase my subjects with SHAPEIT (chr by chr).
The output format is hap and sample files.
How can be these files analyzed and visualized? How to move further?
Options based on my search:
It seems "HAPLOVIEW" can take only "HAPMAP PHASE" format: hap, legend and sample. I was wondering if there is a way to convert SHAPEIT output format to HAPMAP format? What tools can subset a HAPMAP format or SHAPEIT output? I need to analyze only a 200Kb region of chr11.
PLINK1.07 can handle haplotype analysis. However, phasing with PLINK is not recommended. Is there a way to integrate the phased files from SHAPEIT with PLINK.
Is there a way to create "myfile.hlist" from SHAPEIT output for PLINK.
Haplotype testing in PLINK requires that the user supplies a file listing the haplotypes to be tested (Some precomputed lists are given below which might be useful in some circumstances.) The formats of these files are described below. An alternative is to specify a simple, sliding window of fixed haplotype size (also described below). The command: plink --file mydata --hap myfile.hlist
I can use PLINK --recodeHV option to make a linkage file for HAPLOVIEW. How can I phase it? The HAPMAP or GeneCruise tracks are not available anymore for download.
Can I convert the SHAPEIT phased hap and sample files to PLINK files? Would be these files phased PLINK files that could be used with the --block option and other association analysis without the need of "myfile.hlist"?
Sorry for the lenghty post but I would like to really understand haplotype analysis and do it in the proper way.
Any help, guidance, tutorial and recommendation of tools are highly appreciated. Thanks a lot, Anita