Single sampled run

[wjhlang]

Hi all,

I tried to submit a phasing and imputation run on a single sample but was notified that I needed at least 5 samples. Is there a way we can still run a single sample, which was available in Michigan Imputation Server 1?
In addition, I tried to rename and duplicate 5 times the SNPs as a workaround, but was told "File should be phased, but also includes unphased and/or missing genotypes! Please double-check!".

My SNPs look like this:

chr1 279709 . T C 96.64 . BaseQRankSum=-0.967;ExcessHet=3.0103;FS=0;MQ=60;MQRankSum=0;QD=24.16;ReadPosRankSum=0.967;SOR=1.609;DP=20;AF=0.5;MLEAC=1;MLEAF=0.5;AN=10;AC=5 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,3:4:33:0|1:279699_T_C:104,0,33:279699 0|1:1,3:4:33:0|1:279699_T_C:104,0,33:279699 0|1:1,3:4:33:0|1:279699_T_C:104,0,33:279699 0|1:1,3:4:33:0|1:279699_T_C:104,0,33:279699 0|1:1,3:4:33:0|1:279699_T_C:104,0,33:279699

chr1 292249 . C T 68.64 . BaseQRankSum=3.13;ExcessHet=3.0103;FS=0;MQ=60;MQRankSum=0;QD=3.27;ReadPosRankSum=-1.927;SOR=0.074;DP=105;AF=0.5;MLEAC=1;MLEAF=0.5;AN=10;AC=5 GT:AD:DP:GQ:PL 0/1:17,4:21:76:76,0,417 0/1:17,4:21:76:76,0,417 0/1:17,4:21:76:76,0,417 0/1:17,4:21:76:76,0,417 0/1:17,4:21:76:76,0,417

so I do have phased and unphased SNPs in my file, why would I see this error message in this case?

Thank you so much!
Jason

[seppinho]

Thanks for reporting. The current code checks if the first line of the VCF file is phased and stops if subsequent VCF lines are unphased -> see here

This was previously necessary since we decided if phasing should be executed or not. Now, phasing is executed if a phasing engine is selected (see here)

@lukfor I would recommend to remove the check in QC from above. We still have a check for "no-phasing" but input is unphased.

[seppinho]

see changes here: genepi/imputationserver-utils@ace1b08 and #43

[wjhlang]

Thanks for the response and for removing that QC check. Has this change been published to the web tool? I've tried running the job again, but the same error persists: "File should be phased, but also includes unphased and/or missing genotypes! Please double-check!"

[seppinho]

Not yet. If you want to run that immediately, simply replace all | with / in your input file. Alternatively, changing just the first line should do the trick.