Hi all,

I was trying to conduct ROH analysis with bcftools version 1.9. As I don't have any information about allele frequency from my target population, I tried to use -e (or --estimate-AF) to estimate AF:

bcftools roh -e sample.list my_data.vcf > roh.out

Where sample.list contain sample names from my_data.vcf and the vcf file contain both GT and PL.

I found that when sample.list contained all the sample that I had, the program stuck. It will not end and the output file only contained first 3 lines, like:

Number of target samples: 6

Number of --estimate-AF samples: 6

Number of sites in the buffer/overlap: unlimited

However, when I deleted one individual in sample.list, the program ran smoothly without any error message, and the output file looked fine.

Does anyone know what's going on?

A further question is, if I didn't set recombination rate nor give a genetic map (via -M and -m option), what value will be used in bcftools roh analysis by default?

Thanks