How do I merge plink files with different SNPs?
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21 months ago
amber ▴ 10

I've used GATK to call variants from RNA-sequencing data (following the guidelines here), which gives me a vcf file for each sample. I have then converted each vcf to plink format:

./plink2 --vcf file.vcf --make-bed --out plinkfile --allow-extra-chr --chr 1-22 XY --snps-only --max-alleles 2

I'd like to now merge the plink files for each sample so I can carry out an association analysis. However, the problem is that each .bim file has different SNPs, and the overlap in SNPs between each file is 40-50%. As I have many samples to merge, I don't want to exclude non-overlapping SNPs because the number that will overlap between every single sample will be tiny. Is there any way to merge keeping all the SNPs, but coding them as missing?

SNP genome plink vcf • 825 views

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