Unknown chromosome ?

[ptranvan]

Hi, I am trying to use vcf2diploid but I got this error :

Working on Scaffold10...
Unknown chromosome Scaffold10.
Working on Scaffold11...
Unknown chromosome Scaffold11.

...

I don't understand because my fasta header and the vcf match well ..

Is it working with my own genome assembly ?

[abyzov]

Hi Patrick, currently vcf2diploid is only working with canonical (1-22, X, Y) chromosomes of human genome. Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic ----------------------------- Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978 fax: +1-(507)-284-0745 On Oct 7, 2019, at 7:44 AM, Patrick Tran Van <[email protected]<mailto:[email protected]>> wrote: Hi, I am trying to use vcf2diploid but I got this error : Working on Scaffold10... Unknown chromosome Scaffold10. Working on Scaffold11... Unknown chromosome Scaffold11. ... I don't understand because my fasta header and the vcf match well .. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#7?email_source=notifications&email_token=ACLKGONIODDQIKE77BKT2CLQNMVLZA5CNFSM4I6D7WWKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HQBWX4A>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ACLKGOMJAEYJSLCO3X3V3V3QNMVLZANCNFSM4I6D7WWA>.

[kashiff007]

Hi @abyzov,

Will it work if I replace all scaffolds name with number? I have 300 scaffolds.

Thanks,

[abyzov]

Hello, I think it will not. As far as I remember how I implemented the tools it will only work with canonical human chromosomes. Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic ----------------------------- Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

[kashiff007]

One way of doing is to change your scaffold names as chr1, chr2, .... so on. It will work in this way till chr30. If you have scaffolds more than 30 then you have repeat this step.