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Posts by wangdavid758
... I have a VCF file, lets call it file A, which was created by performing variant calling using GATK on whole genome sequencing data. For SNPs that do no appear in the VCF, can I assume that the SNP is monomorphic for the reference allele (i.e all 0 encoding). Note that sites that are monomorphic for ...
... Hi, I have a phased vcf file and I want to recode the reference allele according to be what is a specified in a list. The list is 2 columns: SNP id in the first, and the reference allele I want in the second. For example, if my REF and ALT alleles in the vcf are A and T respectively for SNP rs12345 ...
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