fasta file format not supported

[suvi93]

Hi,

I'm using SHAPEIT5 and I'm getting this error -
ERROR: Opening [ref.fasta]: file format not supported by HTSlib

the command I'm using is as follows -
SHAPEIT5_phase_common -T 16 -I S2_WhPh.vcf.gz -H ref.fasta -R PGA_scaffold_6 -O S2_SH.vcf --log P24XYF_S2_SH.log

what does this error mean exactly?

Thanks!

[srubinacci]

Hi,

When refer to "reference panel" we mean a cohort of haplotypes (e.g. in vcf/bcf format), not the reference genome sequence (in fasta). You are simply providing a wrong file.

You can find some common definitions here, in the hope they are useful: https://odelaneau.github.io/shapeit5/docs/glossary/#reference-panel

Hope this helps,

Simone

[suvi93]

what if i don't have this data? i just tried removing this option and it did not let me run the phasing without it.

this was the new error message -

ERROR: Less than 50 samples is not enough to get reliable phasing, consider using a reference panel to increase sample size

[srubinacci]

Hi,
Unfortunately, population-based statistical phasing needs at least a certain amount of samples to be reliable.

Simone