Question: genotype imputation pipeline
1
gravatar for alessandrotestori7
4.2 years ago by
alessandrotestori7390 wrote:

Hello. I'm trying hard to go through the genotype imputation pipeline, unsuccessfully though. I have .bim .bed and .fam files and I need to select a subset of typed SNPs in these files and impute other SNPs. So far so good. I then prephase using shapeit and impute with impute2. I downloaded .hap.gz .legend.gz and genetic_map* files from the impute2 website (haplotype release date: October 2014). The last step would be running snptest, in order to get association results. Can anyone share his/her own pipeline with me? I get at some point this error: "ERROR: There are no type 2 SNPs after applying the command-line settings... ". I would greatly appreciate a step by step pipeline, since all the above software is already installed on my computer. Please let me know. Cheers, Alessandro

imputation snps gwas • 2.8k views
ADD COMMENTlink modified 4 months ago by Kevin Blighe66k • written 4.2 years ago by alessandrotestori7390
2

There is this a recent paper:

Molgenis-impute: imputation pipeline in a box

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541731/

or a pipeline from github:

https://github.com/CNSGenomics/impute-pipe

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by natasha.sernova3.7k

Thanks, I'll look into it.

ADD REPLYlink written 4.2 years ago by alessandrotestori7390

In any case, I would be very grateful if someone could share even just a fake little example with me. I start from .hap .legend and genetic_map* files I retrieve from Impute2 website and then I use my binary plink format files with genotypes as input. I think this is all I need, since I have installed all necessary software.

ADD REPLYlink written 4.2 years ago by alessandrotestori7390
0
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:
  1. Pre-phasing with SHAPEIT2 ( C: Phasing with SHAPEIT )
  2. Phased imputation with IMPUTE2 ( A: ERROR: You must specify a valid interval for imputation using the -int argument, )
  3. Conversion to VCF (see #2)

Kevin

ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe66k
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