search

grenaud / glactools

command-line tools for the management of genotype likelihoods and allele counts
http://grenaud.github.io/glactools/
GNU General Public License v3.0
29 stars 2 forks source link

shortchanged by acf2betascan #10

Closed jh041 closed 4 years ago

jh041 commented 4 years ago

Hi Grenaud,

I've never had any problem with the glactools acf2betascan conversion before, until today when it is outputting fewer loci than are input.

glactools acf2betascan --fold qt6.acf > qt6.beta.txt Program ACF2BETASCAN looked at 9005 records, terminated gracefully

9005 is the correct number of SNP loci. But...

wc qt6.beta.txt 8961 26883 106058 qt6.beta.txt

Can you help me find where my missing 44 loci went and how to get them back?

grenaud commented 4 years ago

Dear John, I am super swamped for the rest of the week, do you mind if I address this early next week?

Sorry again!

Gabriel

On Thu, Dec 12, 2019 at 8:40 PM John B. Horne notifications@github.com wrote:

Hi Grenaud,

I've never had any problem with the glactools acf2betascan conversion before, until today when it is outputting fewer loci than are input.

glactools acf2betascan --fold qt6.acf > qt6.beta.txt Program ACF2BETASCAN looked at 9005 records, terminated gracefully

9005 is the correct number of SNP loci. But...

wc qt6.beta.txt 8961 26883 106058 qt6.beta.txt

Can you help me find where my missing 44 loci went and how to get them back?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/grenaud/glactools/issues/10?email_source=notifications&email_token=AAQRNI5TFFG7SMR2HKLFSHLQYKHUFA5CNFSM4J2DOS22YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IAEUTKQ, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQRNI7WJOEKUTFT6U4Z3F3QYKHUFANCNFSM4J2DOS2Q .

jh041 commented 4 years ago

Standing by until next week.

grenaud commented 4 years ago

Dear John, my apologies for the delay, I see in the code that it will skip sites where the alternative is not resolved (essentially non segregading site), could you do a "glactools view qt6.acf | grep N"? otherwise, could you send me the acf file via email or send a link to a dropbox?

jh041 commented 4 years ago

Ah, that makes perfect sense. I recently removed some samples from this data, so the 44 loci must have only been polymorphic for that group.

glactools view qt6.acf | grep 'N' | wc 44 16016 96091

I didn't realize that the program would remove such loci, but that is exactly what happened. Thanks for the insight.