i have an overlap between my reference and non-reference sample !

Question

[nour.hadjz]

hello,

My reference file contains individuals from several populations and among these population there are my study individuals "MSL" and I have another vcf file that only contains my "MSL" individual ranging from HG03052 to HG03583

however when I try to impute I have a message that says I have an overlap between reference and non-reference samples

Please can you tell me how to remove MSL individuals ranging from HG03052 to HG03583 from my reference file and have an output file without MSL??

thank you for helping me

[Matteo Schiavinato]

Impute with which tool? What is your reference file format? What are MSL individuals?

[nour.hadjz]

i try to impute with beagle 4.1 my reference file format is chr22.1kg.vcf.gz MSL individuals are sortieMSL.recode.vcf ( African population) this MSL population is in my reference file and I want to remove it and have a reference file without MSL.

[nour.hadjz]

i want juste to remove this MSL population in my reference file which is row from HG03052 to HG03583 individuals, and then only have the reference file without this population.

if you can help me ! thank you.