beagle error: genotype is missing allele separator
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17 days ago
ziv_attia • 0

I am trying to impute a VCF table that was created by GATK and then filtered with VCFtools with beagle. when I run the following code:

file=chr1.vcf java -Xmx144g -jar /home/pogoda/software/BEAGLE/beagle.03Jul19.b33.jar gt=${file} nthreads=36  out=IMPUTED_${file}

I get the following error: ERROR: genotype is missing allele separator: couldn't find any information online, any suggestions? thanks!

genomics imputation bioinformatics • 193 views
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Please can you post a couple of lines of your vcf?

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ERROR: genotype is missing allele separator: Ha412HOChr01 3689738 . G A 1581.21 . AC=20;AF=0.115;AN=174;BaseQRankSum=0.00;DP=465;ExcessHet=1.0924;FS=3.561;InbreedingCoeff=0.0116;MLEAC=25;MLEAF=0.144;MQ=53.36;MQRankSum=-1.150e+00;QD=15.35;ReadPosRankSum=-4.140e-01;SOR=1.088 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:5,0:5:15:.:.:0,15,136:. 0|1:6,2:8:66:0|1:3689736_T_C:66,0,246:3689736 0|1:4,2:7:72:0|1:3689736_T_C:72,0,162:3689736 1|1:0,1:1:3:1|1:3689736_T_C:45,3,0:3689736 0|1:5,1:6:27:0|1:3689736_T_C:27,0,207:3689736 0/0:3,0:3:9:.:.:0,9,99:. 0/0:3,0:3:9:.:.:0,9,65:. 0/0:3,0:3:9:.:.:0,9,91:. 0/0:4,0:4:12:.:.:0,12,141:.0/0:5,0:5:0:.:.:0,0,137:. 0/0:5,0:5:15:.:.:0,15,141:. 0/0:8,0:8:24:.:.:0,24,245:. 0/0:2,0:2:6:.:.:0,6,57:. 0|1:13,4:17:99:0|1:3689736_T_C:118,0,534:3689736 0/0:6,0:6:18:.:.:0,18,170:.0/0:5,0:5:15:.:.:0,15,163:. 0/0:4,0:4:12:.:.:0,12,141:. ./.:0,0:0:.:.:.:0,0,0:. 0/0:6,0:6:18:.:.:0,18,148:. 0|1:12,6:18:99:0|1:3689736_T_C:216,0,486:3689736 0/0:13,0:13:39:.:.:0,39,485:. 0|1:2,2:4:78:0|1:3689736_T_C:78,0,78:3689736 0/0:5,0:5:0:.:.:0,0,125:. 0/0:2,0:2:6:.:.:0,6,57:. 0/0:1,0:1:3:.:.:0,3,15:. 0/0:11,0:11:30:.:.:0,30,450:. 0/0:7,0:7:18:.:.:0,18,270:. 0/0:3,0:3:9:.:.:0,9,91:. 0/0:6,0:6:0:.:.:0,0,133:. 0/0:3,0:3:9:.:.:0,9,99:. 0|1:1,2:3:36:0|1:3689736_T_C:81,0,36:3689736 0/0:6,0:6:18:.:.:0,18,207:. 0/0:4,0:4:12:.:.:0,12,114:. 0|1:7,1:8:21:0|1:3689736_T_C:21,0,291:3689736 0/0:11,0:11:0:.:.:0,0,274:. 0/0:7,0:7:21:.:.:0,21,224:. 1|1:0,2:2:6:1|1:3689736_T_C:90,6,0:3689736 0/0:4,0:4:9:.:.:0,9,135:. ./.:0,0:0:.:.:.:0,0,0:. 0/0:2,0:2:6:.:.:0,6,57:. ./.:1,0:1:.:.:.:0,0,0:. 0/0:3,0:3:9:.:.:0,9,125:. 0/0:3,0:3:9:.:.:0,9,65:. 0/0:3,0:3:9:.:.:0,9,99:. 0|1:7,7:14:99:0|1:3689736_T_C:273,0,273:3689736 .: Exiting Program

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it seems like there are some added characters at the end of each genotyping _T_A:45,3,0:413375

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