Load and i-view a pedigree in pseq

[Michael Gilson]

Greetings, plinkseq-users!

Has anyone successfully loaded a pedigree into a pseq (v 0.10) project, and confirmed the load with i-view?

For example, I started with a pedigree from the plinkseq website (https://atgu.mgh.harvard.edu/plinkseq/input.shtml), which looks like this

0001   .   .   .   .   1

0002   .   .   .   .   2

0003  F1   3   1   2   2

(Note, I've added tabs since that is what pseq expects.)

I add to an empty project with 

pseq proj load-pedigree --file example.ped

And then to verify that it loaded, run

pseq proj i-view

Which returns what looks to be an empty INDDB:

#PHE    .

#STRATA .

#ID     FID     IID     MISS    SEX     PAT     MAT     META

Although, if I connect sqlite3 to the INDDB database, and list the individuals table, the data appears to be there

sqlite> select * from individuals;

1|0001|.|.|.|.|1

2|0002|.|.|.|.|2

3|0003|F1|3|1|2|2

My question is, given the pedigree from the website, is this the expected behavior from i-view?

Cheers,

Michael

[bubson...@gmail.com]

Known individuals from .vcf file doesn't seem to get updated.

I guess we have to edit the database by our own script until the author stops being dead.