Conditional analysis with duplicate variant IDs in PLINK

plink --bfile myplink --extract mysnsp.txt --pheno mypheno.txt --covar mycovar.txt --no-parents --allow-no-sex --missing-phenotype -9 --maf 0.05 --geno 0.05 --hwe 1e-09 --linear --ci 0.95 --condition-list best.txt --out conditional_model

4.1 years ago by

Vincent Laufer • 1.1k

United States

Vincent Laufer • 1.1k wrote:

Depending on what you think about the duplicated positions, I'd either remove them, (based on quality metrics, etc.) recode it as multiallelic, or write a script to give all my RSIDs unique names.

The first two options should be possible using published tools. For the last option, it would look something like:

Let's call it: give_snps_unique_names.py

outfile=open('name_of_output_vcf.vcf', 'a')
    i=0
    position_list=list()
    with open('my_vcf.vcf', 'r') as input_vcf:
            for line in input_vcf:
                    line=line.strip().split()
                    if line[1] in position_list:
                            i+=1
                            line[1]=line[1] + "_" + str(i)
                    else:
                            i=0
                    position_list.append(line[1])
                    print(line)
                    outfile.write("\t".join(line) + "\n")

for the sample data

1 rs4553536 (... and the other vcf columns ...)
2 rs4452526
2 rs5909240
3 rs2480408
4 rs22857424
5 rs47249422
6 chr6:57669955
6 chr6:57669955
6 chr6:57669955
6 chr6:57669955
6 chr6:57669955
7 rs42082904
7 rs82498424
7 rs20948494

python give_snps_unique_names.py

returns:

['1', 'rs4553536', ... (and other cols) ...]
['2', 'rs4452526']
['2', 'rs5909240']
['3', 'rs2480408']
['4', 'rs22857424']
['5', 'rs47249422']
['6', 'chr6:57669955']
['6', 'chr6:57669955_1']
['6', 'chr6:57669955_2']
['6', 'chr6:57669955_3']
['6', 'chr6:57669955_4']
['7', 'rs42082904']
['7', 'rs82498424']
['7', 'rs20948494']

and will write a vcf that should be identical but with no non-unique RSIDs.

May need to include something to deal with the header.

ADD COMMENT • link modified 4.1 years ago • written 4.1 years ago by Vincent Laufer • 1.1k

Thanks for sharing this other workaround, but my question aimed at understanding why the problem appears only with conditional analyses (and not with classical association study) and how to fix the problem without modifying the original data (or re-coding the top-associated SNPs and add it to the covariate set).

ADD REPLY • link written 4.1 years ago by alesssia • 560

because the source code scans input IDs for conditional analysis, but not for single SNP analysis. If you think about how you have to code the conditional analysis, it makes perfect sense why it would do so. https://github.com/chrchang/plink-ng Chris Chang is very responsive, if you have questions about the source code itself I'd try Plink2's user help forums.

ADD REPLY • link modified 4.1 years ago • written 4.1 years ago by Vincent Laufer • 1.1k

Thanks Vincent, will do!

ADD REPLY • link written 4.0 years ago by alesssia • 560

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