confused about bcftools roh --ignore-homref option

Question

[Duarte Molha]

Hi. I am confused about this option on bcftools roh

the inclusion of this parameter (--ignore-homref) leads me to the understanding that if I do not include it bcftools orh command, it will consider homozygotic reference SNPS on my input VCF file for ROH calculation.

However, as homozygotic reference SNPS are not a biallelic site they are ignored whether you use this or not.

Since my design is targeting common snps I would very much like BCFtools to include the homozygotic snps in the analysis but it does not as they are skipped by default as non-biallelic, and this argument changes nothing to the behavior of the program.

Can anyone help explain this to me?

Many thanks

[Pierre Lindenbaum]

However, as homozygotic reference SNPS are not a biallelic site

can you explain this please ?

[Duarte Molha]

Well ... it is of course bialellic ... but it is filtered on BCFtools as non bialellic ... why I am not sure ... that is how they are being reported as filtered

[Duarte Molha]

as an example... here is my command:

bcftools-1.10.2/bcftools roh -G 30' --AF-dflt 0.4 -I -O region loh.vcf > test_roh

Number of target samples: 1

Number of --estimate-AF samples: 0

Number of sites in the buffer/overlap: unlimited

Number of lines total/processed: 28988/20698

Number of lines filtered/no AF/not biallelic/dup: 0/0/8260/1

within that 8260(not biallelic) value are ALL my hom-ref entries on the vcf file