Alternatives to snpflip to find ambigious and flipped snps

Question

[d.s.zimmerman]

Hello everyone,

I having an issue with strand flips when trying to perform imputation. In the past on an old HPC I used it supported snpflip, a tool which would recognize ambigious snps as well as snps that have been flipped. These snps would be output into a list that you could use to remove and/or flip these specific snps. On the knew HPC I work on snpflip is no longer supported and it is virtually impossible to install, I have asked the helpdesk of the HPC however they have policies against installing programs older than 3 years and which aren't supported.

Does anyone know or have any solutions to locate flipped strands and snps in PLINK data? specifically .bed,.bim.fam files. Is there an alternative to this method? I cannot impute my data without resolving these SNPS.

Thanks in advance!

Kind regards,
Dominic

Answer 1

[bk11]

Genotype-Harmonizer could be an alternative option to correct for strand flips in your data. What approach are you using to impute your genotyped data? If you are using Michigan or TOPMed Imputation Servers, this site provides quality control steps your need to perform to prepare your data for the imputation.

[d.s.zimmerman]

Thank you! I am actually using both to compare so I will try these out and let you know if it works.

[d.s.zimmerman]

Hi there, just here to say thank you again. Your solution has worked for me

[GenoMax]

I have moved the original comment to an answer. Feel free to accept the answer (green check mark) to provide closure to this thread.