how to convert from hap/legend to VCF
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Entering edit mode
2.3 years ago
raalsuwaidi ▴ 100

Hi all,

i used the -merge_ref_panels_output_ref option to generate the merged dataset used in a study from two different reference panels. the output is two files, a hap, and a legend file. i need to transform this output to vcf for further study but i can't find the way to do it.

looking at shapeit the input should be hap/leged/sample or hap/sample, and IMPUTE2 does not provide the sample file as part of the output. and i don't know if i should use the sample files for the two original input reference panels used, as i am not sure which samples will still be there in the merged output or in which order!!!?

so my question is this, is there a way to transform the hap/legend set to a vcf file? and if there is no way out of using a sample file, then how can this be generated keeping in mind that IMPUTE2 is generating the merged output based on imputing one reference panel into the other?

thank you all in advance.

-merge_ref_panels_output_ref VCF IMPUTE2 • 1.5k views
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3
Entering edit mode
2.3 years ago

plink2 --haps <full .haps filename> --legend <full .legend filename> --export vcf --out <output filename prefix>

See https://www.cog-genomics.org/plink/2.0/input#haps and https://www.cog-genomics.org/plink/2.0/data#export for details.

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