Reference DB empty

[frani...@gmail.com]

I have downloaded reference databases from https://atgu.mgh.harvard.edu/plinkseq/resources.shtml, placed them in a folder and used --resources when creating my project to indicate where they are. However, it looks like plinkseq doesn't see my REFDB: 

---Reference DB summary---

(empty)

although it sees the others, e.g.: 

---Locus DB summary---

Group : refseq (33234 entries) n/a

---Sequence DB summary---

chr1:1..249250621 MB=249

chr2:1..243199373 MB=243

I really need it to see my reference DB; could you please help me with this?

Best,

Sanja

[yiwey...@gmail.com]

I am having a similar problem.

To recap, this is what I did:

1) downloaded the refdb.dbsnp.gz file from the link on the Plinkseq site, unzipped it
2) pseq proj5 new-project --resources hg19
3) placed unzipped refdb.dbsnp file into the hg19 folder
4) pseq proj5 ref-load --vcf hg19/refdb.dbsnp --group dbsnp --refdb refdb

This gives the error message:
 pseq error : missing header in VCF? error at line:
SQLite format 3@  ??s

and my refdb is empty

Any insights? Thanks!

Yiwey

[Victoria Fernandez]

Hi, I ma having the very same problem... did you come up with any solution?

Thanks

Victoria

[Priya Bhatt]

I'm having the same problem.  Did you find a solution?

[aditya sai]

I had this same issue, you should specify the full path to the refdb and seqdb

for instance

pseq proj new-project --resources hg19/ --refdb hg19/refdb.dbsnp --seqdb hg19/seqdb.hg19