Pedigree in shapeit4?

[tkn132]

Hi,

Does shapeit4 utilize relatedness in haplotype phasing as shapeit2 does (duohmm)? Since shapeit4 use vcf inputs, I assume a 'no'. So how does it be more accurate than the previous version?

Sorry you might already state it somewhere and I miss it.

[odelaneau]

You can build a haplotype scaffold from pedigrees using the program make Scaffold available from there: https://github.com/odelaneau/makeScaffold

Not super well package, but some people managed to use, so I guess it's doable :)

Then see S4 documentation to know how to use a scaffold in analysis.

Best,

Olivier.

[taolincj]

You can build a haplotype scaffold from pedigrees using the program make Scaffold available from there: https://github.com/odelaneau/makeScaffold

Not super well package, but some people managed to use, so I guess it's doable :)

Then see S4 documentation to know how to use a scaffold in analysis.

Best,

Olivier.

Hi, Olivier Would you like to provide a link for S4 documentation? Sorry you might already state it somewhere and I miss it.

If I run makeScaffold using a phased VCF generated by shapeit4 as an input file, it means the phased VCF will be further corrected by providing a pedigree?

Thank you very much!

Lin Tao

[odelaneau]

Hi,

This is a two steps procedure:

(1) You feed makeScaffold with a VCF containing the genotype data for your duos/trios, together with a fam file describing the family structure. MakeScaffold will phase all non-triple hets using trio information and partially phase the VCF file.

(2) Use the resulting VCF file as argument for SHAPEIT4 --scaffold option. S4 will statistically phase all remaining genotypes on top the scaffold.

Hope this helps,

Olivier