recode pgen file to specific ref-alt

[Giulia Pontali]

Hi,
we write to you because we encountered some problems when we try to recode the pgen file to different reference allele (alphabetical order) and then when we compute the --freq, it seems that the actual code of pgen file is not updated. We were expecting that the new frequency would be updated when the alleles are flipped. 

We attach an example with the respective code that we used to illustrate the step and the problem. 

Please let us know if you have some suggestions to how we can proceed.
Thank you,
Giulia 

[Chris Chang]

You did not use the correct flag.

https://www.cog-genomics.org/plink/2.0/data#ref_allele

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[Giulia Pontali]

Thank you for your reply, so basically to update the SNP ids, the alleles labels and recode genotypes do we need three steps?
1. Update SNP ids with --update-name:

plink2 \
--update-name {params.table_mapping} 1 2 \
--pfile {params.pfile} \
--make-pgen \
--out {params.prefix} \
--threads {resources.threads} \
--memory 1900 'require'

2. Update allele labels with --update-alleles:

plink2 \
--update-alleles {params.mapping_table_right_alleles} \
--make-pgen \
--pfile {params.pfile} \
--out {params.out_file} \
--threads {resources.threads} \
--memory 1900 'require'

3. Recode the pgen with --ref-allele:

plink2 \
--ref-allele {params.mapping_table_right_alleles} 1 4 \
--make-pgen \
--pfile {params.pfile} \
--out {params.out_file} \
--threads {resources.threads} \
--memory 1900 'require'

However when we compute the --freq from the last file we still have the freq related to the old effect allele.
Thank you for your advice

[Chris Chang]

You are probably misusing —update-alleles.

[Giulia Pontali]

So what do you suggest to do? When we update the alleles using --update-alleles (this works) then plink2 does not recode the genotype.

[Chris Chang]

More precisely, you probably shouldn’t use —update-alleles at all.  It is doing exactly what it is documented to do.  I already told you that you are using the wrong flag, and what flag(s) to be using INSTEAD, not IN ADDITION.

[Giulia Pontali]

Thank you.
Using the command that you suggest to me works, but the genotype still has not been updated.

plink2 \
--ref-allele snp_mapping_right_alleles_2.tsv 1 4 \
--alt1-allele snp_mapping_right_alleles_2.tsv 1 2 \
--make-pgen \
--pfile impute_recoded_selected_sample_filter_hq_var_new_id_alleles_2 \
--out 2_test \
--threads 8 \
--memory 1900 'require'

[Chris Chang]

Please provide a replicable example (could be a dataset with just one variant) of a genotype that you think should be updated, but isn’t.

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