acf2betascan empty output

Question

acf2betascan empty output

josieparis opened this issue 5 years ago · 6 comments

josieparis commented 5 years ago

Hey grenaud,

I am getting an empty output for acf2betascan:

glactools acf2betascan --useanc ../acf_files/APHP_holi13.acf > APHP_beta.freq

it seems to have run fine:
Program ACF2BETASCAN looked at 5171179 records, terminated gracefully

Any ideas?

Thanks!

Answer 1 · 2019-05-15T18:52:47.000Z

Hi josieparis,
Is the ancestral state defined?

Gabriel

Answer 2 · 2019-05-16T12:39:21.000Z

Hey Gabriel,

Thanks for getting back to me so quick. I have the ancestral state defined in the vcf file like so:
chr1 4620 chr1_4620 A G 5527.83 PASS AA=A
chr1 4827 chr1_4827 G A 38420.2 PASS AA=G
chr1 4947 chr1_4947 T G 6433.52 PASS AA=T
chr1 5182 chr1_5182 A C 5021.24 PASS AA=A

It also does not produce an output when I use --useroot

Answer 3 · 2019-05-16T13:01:19.000Z

Ok the conversion to ACF cannot process custom tags for now. You could add it as a feature request.

For now you could either:

if this is hg18, you could use our per-parsed EPO files during acf conversion
otherwise, get a VCF of the ancestral state and use replaceanc+usepopsrootanc to use it as ancestral
or specify --fold but then you lose which allele is ancestral and derived, you just get minor/major.

Answer 4 · 2019-05-16T13:22:03.000Z

ah gotya!

yeah unfortunately these are custom vcfs. I'll add as a feature request

in the meantime, I'll probably just fold them.
thanks for your help! (and glactools - very useful)

Answer 5 · 2019-05-16T13:23:30.000Z

Ok for now, may I close this issue? tor. 16. maj 2019 16.22 skrev josieparis <notifications@github.com>:

…

ah gotya! yeah unfortunately these are custom vcfs. I'll add as a feature request in the meantime, I'll probably just fold them. thanks for your help! (and glactools - very useful) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AAQRNI6WPGDDCESLHIGZI4LPVVNXXA5CNFSM4HNFH3KKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVRZHAY#issuecomment-493065091>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAQRNI3BKQZ4FB2OM6JL23TPVVNXXANCNFSM4HNFH3KA> .

Answer 6 · 2021-11-26T03:33:39.000Z

Ok for now, may I close this issue? tor. 16. maj 2019 16.22 skrev josieparis notifications@github.com:
…
ah gotya! yeah unfortunately these are custom vcfs. I'll add as a feature request in the meantime, I'll probably just fold them. thanks for your help! (and glactools - very useful) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AAQRNI6WPGDDCESLHIGZI4LPVVNXXA5CNFSM4HNFH3KKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVRZHAY#issuecomment-493065091>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAQRNI3BKQZ4FB2OM6JL23TPVVNXXANCNFSM4HNFH3KA .

hello grenaud! your reply was helpful. now, I just have outgroup vcf file (other mammals not human), could you tell me how can I transform vcf file to epo file?