Shapeit2 cannot open reference panel
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20 months ago
sunnysean ▴ 20

Hi, I am trying to use shapeit2 for imputation like this:

shapeit --input-bed test \
         --input-map chr20.map \
     --input-ref  chr20.hap.gz, chr20.legend.gz, phase3.sample \
     --output-max  phased.haps, phased.sample

But shapeit2 always return "chr20.hap.gz is impossible to open, check file existence or reading permission". chr20.hap.gz are there, and I couldn't find any error with using "less -S chr20.hap.gz" to check it.

Thanks

gwas shapeit2 phasing • 343 views
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20 months ago

Please remove the commas on your --input-ref line, and also the --output-max line.

I show examples of how to run SHAPEIT here: C: Phasing with SHAPEIT

Kevin

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Thank you! Great help!

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