[REQUEST] Flip-scan with D'

[JoniColeman]

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'