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tl;dr - it would be useful if there were an option for using D' instead of correlation for --flip-scan.
--flip-scan is a useful tool in quality control for identifying flipped ambiguous SNPs when component parts of a GWAS have been genotyped separately. It can also be used to identify variants that have been miscalled during genotyping, as they (may) depart from the expected pattern of LD with neighbouring SNPs. To some extent, this is captured by --flip-scan's current correlation-based measure. However, D' might be a more useful measure here, as it is more sensitive to the presence of unlikely haplotypes. As such, it would be useful if --flip-scan had a D' mode as well.
Ideally, the output would be a variant of that from --flip-scan verbose
CHR_INDX Chromosome code
SNP_INDX Index variant identifier
BP_INDX Index variant base-pair coordinate
A1_INDX Index variant allele 1
SNP_PAIR Second variant identifier
BP_PAIR Second variant base-pair coordinate
A1_PAIR Second variant allele 1
D_PRIME_A Case-only D'
D_PRIME_U Control-only D'
The text was updated successfully, but these errors were encountered:
tl;dr - it would be useful if there were an option for using D' instead of correlation for --flip-scan.
--flip-scan is a useful tool in quality control for identifying flipped ambiguous SNPs when component parts of a GWAS have been genotyped separately. It can also be used to identify variants that have been miscalled during genotyping, as they (may) depart from the expected pattern of LD with neighbouring SNPs. To some extent, this is captured by --flip-scan's current correlation-based measure. However, D' might be a more useful measure here, as it is more sensitive to the presence of unlikely haplotypes. As such, it would be useful if --flip-scan had a D' mode as well.
Ideally, the output would be a variant of that from --flip-scan verbose
The text was updated successfully, but these errors were encountered: