Filter palindromic SNPs

[kaustubh...@gmail.com]

Hi Chris,

Would you be able to add a flag to filter out palindromic SNPs in Plink 1.9 and 2?

Like --flip, it might be useful to add a 'permissive' option to retain non-SNP variants.

Also there would be corner cases when a variant is monomorphic in a ped/map file, so when imported to later Plink versions the second allele is 0. I guess those should be allowed to remain.

Thanks,

Kaustubh.

[Chris Chang]

Today's plink2 build has a --exclude-palindromic-snps flag; let me know if you have any problems with it.

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