imputing haplotypes from variants in a VCF file – vcfIndexFile
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
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