smcpp.commands.vcf2smc WARNING Multiple entries found at 13 positions; skipped all but the first

[Keerlllws]

hi @terhorst

I encountered this problem while running smc++. I checked the VCF file and did not find any duplicate SNP sites. Additionally, the VCF file contains only SNP information. How should I resolve this issue?

[Marh32]

I encountered the same issue. This situation occurs because the end position (third column) of your mask bed file is the same as the position in your VCF file, which causes this warning. You can check if there are 13 duplicate positions in the third column of your BED file that match the third column in your VCF file