Added VCF handling #2
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| // std::cout << "Processing sample " << indx << ", SNP " << s << std::endl; | ||
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| if (field[0] == '0' || field[0] == '.') | ||
| snp->one[indx] = 0; // Reference allele (0) |
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we need to make this part of the logic consistent
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In particular, this is the logic we should follow:
Line 1497 in 15ea376
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I followed the logic you suggested. It's still giving me a different output in comparison to the bfile.
I also want to confirm if you run the program with a --bfile and --file flag for the same data would it give the same output?
Below is the code I wrote:
int code = -9; if (field[0] == '.' || field[2] == '.') { code = -9; } else if (field[0] == '0' && field[2] == '0') { code = 0; // Homozygous reference (0/0) } else if ((field[0] == '0' && field[2] == '1') || (field[0] == '1' && field[2] == '0')) { code = 1; // Heterozygous (0/1) } else if (field[0] == '1' && field[2] == '1') { code = 2; // Homozygous alternate (1/1) } else { std::cerr << "Error: unrecognized genotype format: " << field << std::endl; exit(1); }
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can you add your code as a commit to this PR?
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@radioactive17 the internal representatino neends to be changed as well. meaning this part of the code needs to be changed as well.
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Yes, I haven't changed that part of the code. I'll do that and add the updated code. Thanks.
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This pull request introduces updates to handle genotype data from a vcf format
Please review the readVcfData function in the snpdt.cpp file. This function reads data from a VCF file and aims to store it in a format similar to BFILE data (.bim, .bed, .fam).
The primary difference between VCF and BFILE formats lies in how missing genotype data is represented and handled:
In VCF, missing data is explicitly marked with a "."
For example:
In BFILE, missing data is encoded in a binary format (e.g., "01"), which does not specify whether the reference or alternate allele is missing.
This distinction in handling missing data could be introducing discrepancies in statistical calculations, particularly in variants where missing genotypes are prevalent.
I’d like your insights on whether the handling of missing data in this function could be improved to mitigate potential discrepancies. Let me know if further clarification is needed!