Hi all,
I'm trying to build a custom reference panel for use with IMPUTE2. I have a phased .vcf from all my participants, and I was using the first script here, modified slightly to work with my vcf/HG38, to build the reference panel. The exact command I run to generate the files for chromosome 1 (as an example) is:
./vcf2impute_legend_haps.pl -vcf my_vcf.vcf.gz \
-leghap output_prefix \
-chr chr1 \
-hg38
The -hg38 thing is just an argument I added to the script, and can be ignored.
This generates .hap.gz files, .legend.gz files, and .sample_list files, one for each chromosome. What I'm missing is a genetic map file. I don't what these are, and I can't find anything on it in the documentation. Looking at the 1000 Genomes HG37 reference panel files provided here, it's not clear to me what these mapping files are, so I can't replicate the steps to create them.
Any advice would be appreciated.
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written
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john.michel.rouhana •
According to the documentation you linked, genetic maps are recombination maps, measured in centiMorgans.
If you can lift-over the genomic position of the markers from the 1000 Genomes HG37 reference panel, you can use the same genetic map position (the Genetic_Map(cM) column), and recalculate the recombination rate between current position and next position in map (the COMBINED_rate(cM/Mb) column).
However, are you sure there isn't an updated version of these files?
I tried to find updated versions. What you say makes sense, and is actually the conclusion I came to (I missed the response). Once I revisit this problem I'll likely be resorting to recalculating the recombination rates if I cannot find updated files.
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Did you ever get impute2 working with hg38 coordinates?
https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/ I found this genetic map file that contains all autosomes and Chr X in HG38 coordinate.
Hi. The genetic map you posted is provided by Eagle, but it can be use with IMPUTE2 too right? I'm rather new to imputation, so I want make sure. Thanks.