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RADIOMUMM opened this issue Nov 17, 2022 · 5 comments
Open

Some questions about input file making #73

RADIOMUMM opened this issue Nov 17, 2022 · 5 comments

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@RADIOMUMM
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Hi Robbie,
I'm a little confused about pos files.
What did this file generate from those files? Is it a reference panel or a VCF file after variant calling?
But if it is generated from a VCF file after variant calling, is the site "3 42331 A G,T" removed?

Best
jennis
@rwdavies
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Owner

Hi,

pos contains the list of sites you want to impute. One potential source of that is after initial variant calling and filtering. If you have a VCF list of sites you can make the pos file using code something like the following, possibly changing the header to match what's asked for

gunzip -c sites.vcf.gz | cut -f1,2,4,5 > pos.txt

The site "3 42331 A G,T" will not be accepted by STITCH as STITCH can only impute bi-allelic variants for now. So you could do "3 42331 A G" or "3 42331 A T" but not both G and T

Best,
Robbie

@RADIOMUMM
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RADIOMUMM commented Nov 18, 2022 •
edited
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Hi，

Thanks for your answer, but I have another question:
If I do not do variant calling by chromosomes, then the processed pos file will be a file containing all bi-allelic SNP of 1-12 chromosomes, but STITCH is indeed imputed by chromosome, is there any good suggestion?

Best,
jennis

@suhuan0327
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Hi，

Thanks for your answer, but I have another question: If I do not do variant calling by chromosomes, then the processed pos file will be a file containing all bi-allelic SNP of 1-12 chromosomes, but STITCH is indeed imputed by chromosome, is there any good suggestion?

Best, jennis

HI,

I have the same issue, how did you solve it.

Thanks,
Su

@rwdavies
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Owner

I think in this instance, I would just split the file into one file per chromosome, and impute each chromosome seperately

Something like

for CHR in `echo 1 2 3`
do
  gunzip -c sites.vcf.gz ${CHR} | cut -f1,2,4,5 > pos.${CHR}.txt
  # impute here using pos.${CHR}.txt
done

@suhuan0327
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I think in this instance, I would just split the file into one file per chromosome, and impute each chromosome seperately

Something like

for CHR in `echo 1 2 3`
do
  gunzip -c sites.vcf.gz ${CHR} | cut -f1,2,4,5 > pos.${CHR}.txt
  # impute here using pos.${CHR}.txt
done

Hi,

Thank you for your reply, and I also used the same way to deal with my files.

Best,
Su

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@rwdavies @RADIOMUMM @suhuan0327
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