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BenjaminPeter / admixfrog

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PanTro4 reference #4

Closed CLeib closed 2 years ago

CLeib commented 2 years ago

Hi, How was the pseudo haploid panTro4 reference sample created for the reference file? Thanks, Chen

JielinLi commented 3 months ago

Hi, Have you solved the problem? I also have the same issue.

CLeib commented 3 months ago

Hi, I ended up using python module MafIO to get the chimp genotype for each position in my VCF from MAF files (downloaded from UCSC), and then using bcftools convert to turn it into a VCF. I'm sure there is a better way to do this, as this is quite time consuming, but it was the best I was able to come up with.

JielinLi commented 3 months ago

Hi, You explained it very clearly, I understand now. Thank you so much!

JielinLi commented 2 months ago

Hi, I want to ask if your file is like this:

22 17032698 T
22 17054720 C
22 17057138 A
22 17075353 C

the first column is the chromosome, the second column is the position of hg19 and the third columns is the pantro5 genotype in this position. Thank you so much!

CLeib commented 2 months ago

Hi,

Yes, that's it :)

If you wish to convert it into a VCF, you can now use: bcftools convert -c CHROM,POS,AA --tsv2vcf <mafIO_output.tsv> -f <hg19_ref.fasta> -s <sample_name> -o <output_name>

JielinLi commented 2 months ago

Hi,

I made it. Thank you so much!