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?
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:104,0,33:279699chr1 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 0/1:17,4:21:76:76,0,417so 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