Comments (4)
grenaud
commented on July 1, 2024
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 ***@***.***> 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?
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jh041
commented on July 1, 2024
Standing by until next week.
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grenaud
commented on July 1, 2024
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?
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jh041
commented on July 1, 2024
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.
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