Robin J. Hofmeister comments

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                                            Robin J. Hofmeister

No variant found

Hi niv280, Can you share the shapeit5 command that you used, and the log file? Thanks, Robin

No variant found

Hi niv280, Your ALT allele must be A,C,T or G for SNPs, or INDELS, but not "" (eg. your ref panel).

No variant found

Hi [michal-yoles](https://github.com/michal-yoles), Try using region=chr6 instead of region=6. Best, Robin

Hi [michal-yoles](https://github.com/michal-yoles), You also need to add the AN tag. AC and AN are used to compute allele frequency. You can easily fill those tags, eg. using bcftools +fill-AN-AC. Cheers

Plot phasing results

Hi [michal-yoles](https://github.com/michal-yoles), This figure can be obtained only if you have a validation set (i.e parent-offspring duos or trios), which allows you to estimate your switch errors. Documentation can be...

Phase_common: AC field is needed in file

Hi, AC field is required because it is the Allele Count field, which is used to compute allele frequency and keep only common variants above the selected threshold. If your...

Outdated path file in tutorial

Hi @lcsfaria , It is indeed the correct file, we changed folders and forgot to update the tutorials. Best, Robin