unknown genotype in a vcf file

Question

[sagardesai91]

I recently came across a vcf file with the following genotypes : "0/2/1" AND "0/2/3/1" what do these mean? Can anybody explain?

[Kevin Blighe]

Please paste the full record / line on which you find these genotypes.

[sagardesai91]

Pasting the full line below:

chr1    13782913        .       CTT     C,CT    .       my_filters      DP=107;ECNT=1;POP_AF=5.000e-08,5.000e-08;P_CONTAM=0.00;P_GERMLINE=-3.402e+00,-2.508e+00;RPA=16,14,15;RU=T;STR;TLOD=5.01,11.14;ANN=C|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_012231.4|protein_coding|8/9|c.5036+97_5036+98delTT||||||INFO_REALIGN_3_PRIME,CT|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_012231.4|protein_coding|8/9|c.5036+98delT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_001135610.1|protein_coding|6/7|c.511+33441_511+33442delTT||||||INFO_REALIGN_3_PRIME,CT|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_001135610.1|protein_coding|6/7|c.511+33442delT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_015866.4|protein_coding|8/8|c.5036+97_5036+98delTT||||||INFO_REALIGN_3_PRIME,CT|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_015866.4|protein_coding|8/8|c.5036+98delT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_001007257.2|protein_coding|3/3|c.4433+97_4433+98delTT||||||INFO_REALIGN_3_PRIME,CT|intron_variant|MODIFIER|PRDM2|PRDM2|transcript|NM_001007257.2|protein_coding|3/3|c.4433+98delT||||||INFO_REALIGN_3_PRIME;DEL;HET;VARTYPE=DEL,DEL     GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB  0/1/2:24,6,9:0.255,0.302:39:14,4,6:10,2,3:27,24,22:133,169,161:42,42:34,28:0.222,0.182,0.231:0.011,0.034,0.955

Answer 1

[finswimmer]

0/1/2 describes the genotype of your sample. 0 means REF, values greater 0 reference to the value in the ALT column.

So 0/1/2 would mean your sample has the genotype CTT/C/CT, which would be triploid. Could this be? If not, how was this vcf file created?

[sagardesai91]

Yes! This makes sense, thank you so much. The vcf file was created using the standard GATK pipeline