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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
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fasta file format not supported #61

Closed suvi93 closed 9 months ago

suvi93 commented 10 months ago

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 commented 10 months ago

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 commented 10 months ago

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 commented 9 months ago

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

Simone