error while running job in michigan imputation server

Question

[rheab1230]

Calculating QC Statistics

Statistics:
Alternative allele frequency > 0.5 sites: 337,476
Reference Overlap: 38.98 %
Match: 5,762,722
Allele switch: 0
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: 63,834
Duplicated sites: 21
NonSNP sites: 0
Monomorphic sites: 42,420
Allele mismatch: 35,561
SNPs call rate < 90%: 0

Excluded sites in total: 141,836
Remaining sites in total: 5,762,722
See snps-excluded.txt for details
Typed only sites: 9,075,374
See typed-only.txt for details

Warning: 32 Chunk(s) excluded: reference overlap < 50.0% (see chunks-excluded.txt for details).
Remaining chunk(s): 0
Error: No chunks passed the QC step. Imputation cannot be started!

I know that the reference overlap is less than 50 and thats why the job is not running. But my vcf genome build is hg19 only.

This is the header of my vcf file:
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20150218
##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
##source=1000GenomesPhase3Pipeline
##contig=<ID=1,assembly=b37,length=249250621>
##contig=<ID=2,assembly=b37,length=243199373>
##contig=<ID=3,assembly=b37,length=198022430>
##contig=<ID=4,assembly=b37,length=191154276>
##contig=<ID=5,assembly=b37,length=180915260>
##contig=<ID=6,assembly=b37,length=171115067>
##contig=<ID=7,assembly=b37,length=159138663>
##contig=<ID=8,assembly=b37,length=146364022>
##contig=<ID=9,assembly=b37,length=141213431>
##contig=<ID=10,assembly=b37,length=135534747>
##contig=<ID=11,assembly=b37,length=135006516>
##contig=<ID=12,assembly=b37,length=133851895>
##contig=<ID=13,assembly=b37,length=115169878>
##contig=<ID=14,assembly=b37,length=107349540>
##contig=<ID=15,assembly=b37,length=102531392>
##contig=<ID=16,assembly=b37,length=90354753>
##contig=<ID=17,assembly=b37,length=81195210>
##contig=<ID=18,assembly=b37,length=78077248>
##contig=<ID=19,assembly=b37,length=59128983>
##contig=<ID=20,assembly=b37,length=63025520>
##contig=<ID=21,assembly=b37,length=48129895>
##contig=<ID=22,assembly=b37,length=51304566>
##contig=<ID=GL000191.1,assembly=b37,length=106433>
##contig=<ID=GL000192.1,assembly=b37,length=547496>
##contig=<ID=GL000193.1,assembly=b37,length=189789>
##contig=<ID=GL000194.1,assembly=b37,length=191469>
##contig=<ID=GL000195.1,assembly=b37,length=182896>
##contig=<ID=GL000196.1,assembly=b37,length=38914>
##contig=<ID=GL000197.1,assembly=b37,length=37175>
##contig=<ID=GL000198.1,assembly=b37,length=90085>
##contig=<ID=GL000199.1,assembly=b37,length=169874>
##contig=<ID=GL000200.1,assembly=b37,length=187035>
##contig=<ID=GL000201.1,assembly=b37,length=36148>
##contig=<ID=GL000202.1,assembly=b37,length=40103>
##contig=<ID=GL000203.1,assembly=b37,length=37498>
##contig=<ID=GL000204.1,assembly=b37,length=81310>
##contig=<ID=GL000205.1,assembly=b37,length=174588>
##contig=<ID=GL000206.1,assembly=b37,length=41001>

[rheab1230]

Is assembly b37 same as hg19? I am not able to see if I can get liftover chain file from b37 to hg19.

[Sasha]

It seems that the issue is related to the low reference overlap in your VCF file. To resolve this issue, you can try the following steps:

1. Make sure that your VCF file is properly sorted. You can use bcftools to sort your VCF file:

   bcftools sort input.vcf -Oz -o sorted_input.vcf.gz
   

2. Check if your VCF file has any duplicate or multiallelic sites, as they can cause issues during the imputation process. You can use bcftools to filter out these sites:

   bcftools norm -m -any sorted_input.vcf.gz -Oz -o normalized_input.vcf.gz
   

3. Ensure that your VCF file has the same chromosome naming convention as the reference panel used by the Michigan Imputation Server. If your VCF file uses "chr" prefix (e.g., chr1, chr2, etc.), you can remove the prefix using the following command:

   zcat normalized_input.vcf.gz | sed 's/^chr//' | bgzip -c > no_chr_normalized_input.vcf.gz
   

4. After performing these steps, try submitting your VCF file to the Michigan Imputation Server again.

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