--a1-allele (plink 1.9)
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Maria Luisa de Barros Rodrigues
May 16, 2022, 10:27:33 AM5/16/22
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I need to merge data in vcf format, but there are some allele mismatches. I tried to fix it in two different ways:
- I used --flip ID_list.txt --keep-allele-order for part of the markers.
- for others, I tried to do an allele swap using the command:
$ plink --vcf MEGA_2.vcf --a1-allele MEGA_swap2.recode.vcf 4 3 '#' --double-id --recode vcf --out MEGA_3
I'm in doubt about the functioning of this second command, because I would like to swap only a few positions, so I put two different inputs, imagining that it would correct the alleles of the second file in the first. This did not work, as the differences between the files increased after this command instead of decreasing, ie other alleles that were already correct were also modified.
how could i swap specific positions or ids as with the flip command?
Or how else could I standardize reference and alternate alleles across different databases?
- I used --flip ID_list.txt --keep-allele-order for part of the markers.
- for others, I tried to do an allele swap using the command:
$ plink --vcf MEGA_2.vcf --a1-allele MEGA_swap2.recode.vcf 4 3 '#' --double-id --recode vcf --out MEGA_3
I'm in doubt about the functioning of this second command, because I would like to swap only a few positions, so I put two different inputs, imagining that it would correct the alleles of the second file in the first. This did not work, as the differences between the files increased after this command instead of decreasing, ie other alleles that were already correct were also modified.
how could i swap specific positions or ids as with the flip command?
Or how else could I standardize reference and alternate alleles across different databases?
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