Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
Hi,
Could you please explain if there is any solution for this error for the X chromosome (all other chromosomes worked fine):
Warning: 8 Chunk(s) excluded: at least one sample has a call rate < 50.0% (see chunks-excluded.txt for details).
Remaining chunk(s): 0
Error: No chunks passed the QC step. Imputation cannot be started!
Hi, Could you please explain if there is any solution for this error for the X chromosome (all other chromosomes worked fine): Warning: 8 Chunk(s) excluded: at least one sample has a call rate < 50.0% (see chunks-excluded.txt for details). Remaining chunk(s): 0 Error: No chunks passed the QC step. Imputation cannot be started!
Chunk SNPs (#) Reference Overlap (%) Low Sample Call Rates (#)
chunk_X.nonPAR_0000000001_0020000000 1035 0.9961612284069098 3 chunk_X.nonPAR_0020000001_0040000000 1237 0.9955375253549695 3 chunk_X.nonPAR_0040000001_0060000000 614 0.993798449612403 3 chunk_X.nonPAR_0060000001_0080000000 455 0.9924160346695557 3 chunk_X.nonPAR_0080000001_0100000000 562 0.9975 3 chunk_X.nonPAR_0100000001_0120000000 773 0.9974358974358974 3 chunk_X.nonPAR_0120000001_0140000000 917 0.9956942949407965 3 chunk_X.nonPAR_0140000001_0160000000 939 0.9947061937533086 3
All other chromosomes worked fine so I was not confident about bad-quality genotyping.
Thanks, Bose