imputing haplotypes from variants in a VCF file

imputing haplotypes from variants in a VCF file – vcfIndexFile

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HI there,

trying to get my PHG imputation pipeline running.

In the configuration file example for “imputing haplotypes from variants in a VCF file”, one parameter is indexFile=/phg/outputDir/vcfIndexFile

Where should I derive this vcfIndexFile?

Or, is it generated by the pipeline (it is located in the outputDIr, so maybe?)

Also,

inputType=vcf

keyFile=/phg/readMapping_key_file.txt

readMethod=UNASSIGNED

vcfDir=/phg/inputDir/imputation/vcf/

countAlleleDepths=true

is readMethod required? Here, I want to use variants in a vcf, so no reads are being used, I think? So do I need this parameter, or the readMapping_key_file.txt?

Sorry if I am misunderstanding obvious points.

Best wishes
Matt Shenton


practical


graph


haplotype


vcf


imputation


PHG

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