Entering edit mode
9 weeks ago
Najla • 0
This is the first time I use Michigan Imputation Server. My imputation worked as it should on all chromosomes (1 to 22) apart from chromosome 9, where the job starts and then it fails and I don't know why and how to fix this issue. Here are some details of my job to give you an idea of the situation.
Input Validation 1 valid VCF file(s) found. Samples: 795 Chromosomes: 9 SNPs: 2997 Chunks: 7 Datatype: unphased Build: hg19 Reference Panel: apps@1000g-phase-3-v5 (hg19) Population: mixed Phasing: eagle Mode: imputation Rsq filter: 0.3 Quality Control Skip allele frequency check. Calculating QC Statistics Statistics: Alternative allele frequency > 0.5 sites: 0 Reference Overlap: 99.97 % Match: 2,127 Allele switch: 860 Strand flip: 0 Strand flip and allele switch: 0 A/T, C/G genotypes: 0 Filtered sites: Filter flag set: 0 Invalid alleles: 0 Multiallelic sites: 0 Duplicated sites: 0 NonSNP sites: 0 Monomorphic sites: 0 Allele mismatch: 9 SNPs call rate < 90%: 2,502 Excluded sites in total: 2,511 Remaining sites in total: 485 See snps-excluded.txt for details Typed only sites: 1 See typed-only.txt for details Warning: 1 Chunk(s) excluded: < 3 SNPs (see chunks-excluded.txt for details). Remaining chunk(s): 7 Pre-phasing and Imputation Chr 9 Imputation on chromosome 9 failed. Imputation was stopped.
Any idea on why to fix this issue?