is_indel about polyfun

[omerwe]

Hi Jerome,

This is the intended behavior. indels cannot be flipped like regular SNPs, because the flip implies a different meaning. Specifically, T->TGTG is an insertion, TGTG->T is a deletion. If we allow for flips, we cannot distinguish between them. For example, if the reference has TGTG and you see a variant T->TGTG in your sumstats, and you allow for flips in the allele order, it could mean two things:

1. An individual has TGTGGTG in that locus
2. An individual has T in that locus

You cannot distinguish between these two options, unless the order of the alleles is preserved between the sumstats and the reference file.

Cheers,

Omer

[jerome-f]

Got it. Thanks for the clarification Omer. I appreciate it. Best Jerome

On Sun, Mar 14, 2021 at 1:39 AM Omer Weissbrod ***@***.***> wrote: Hi Jerome, This is the intended behavior. indels cannot be flipped like regular SNPs, because the flip implies a different meaning. Specifically, T->TGTG is an insertion, TGTG->T is a deletion. If we allow for flips, we cannot distinguish between them. For example, if the reference has TGTG and you see a variant T->TGTG in your sumstats, and you allow for flips in the allele order, it could mean two things: 1. An individual has TGTGGTG in that locus 2. An individual has T in that locus You cannot distinguish between these two options, unless the order of the alleles is preserved between the sumstats and the reference file. Cheers, Omer — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHBV7KX5N7TXYNUG6O2TNJLTDR76HANCNFSM4ZEYAUUQ> .

-- Best Jerome