Parental information for phasing

[HJeffery]

Hi,

The preprint mentions that parental information can be used by the tool but it is not clear where this can be given in the help documentation and how you tell the tool what relation the data is. Ideally I'd like to give it to the all subcommand, would this be possible?

Thank you!

[MeHelmy]

Thank you for reaching, sorry for missing that in the document. I will update it.

In the config.yaml file under this section:

# Update SNPs
#############
update_snps: False
paternal_snps: ""
maternal_snps: ""

You need to set update_snps field to True and as indicated also update the paternal_snps with the full path of the paternal SNPs (bgziped and indexed); ex: paternal_snps: "/home/mydir/parental_snps.gz", also update maternal_snps by adding the full path to maternal SNPs. While it is not available now to use it from subcommad "Ideally I'd like to give it to the all subcommand", but I will add that asap and update you.

Best,
Medhat

[HJeffery]

Thank you very much!