TOPMed Imputation - More than 10000 allele switches

Question

[Akshaj]

I am attempting to impute using the TopMED server, and have followed their data setup pathway. When I ran the imputation, I got the following error message:

**Statistics:
Alternative allele frequency > 0.5 sites: 190,061
Reference Overlap: 98.42 %
Match: 878
Allele switch: 269,268
Strand flip: 0
Strand flip and allele switch: 0
A/T, C/G genotypes: 1,721
Filtered sites:
Filter flag set: 0
Invalid alleles: 0
Multiallelic sites: 0
Duplicated sites: 0
NonSNP sites: 0
Monomorphic sites: 0
Allele mismatch: 95
SNPs call rate < 90%: 0

Excluded sites in total: 269,363
Remaining sites in total: 2,599
See snps-excluded.txt for details
Typed only sites: 4,356
See typed-only.txt for details

Warning: 241 Chunk(s) excluded: < 20 SNPs (see chunks-excluded.txt for details).
Warning: 2 Chunk(s) excluded: reference overlap < 50.0% (see chunks-excluded.txt for details).
Remaining chunk(s): 65
Error: More than 10000 allele switches have been detected. Imputation cannot be started!**

I am unsure of what exactly is causing this. I saw this post but it is 6y old.

Is this the correct strategy to try, or is there something else I can do to determine and/or solve the problem?

Thanks!

[Qianshu]

Hi,

I have the same error with you, have you sorted it out yet? If you have, could you please share some?

Thank you!