dot in the ALT column

[Emma jiang]

Hi all,

My VCF file produced by lobSTR allelotype contains many lines like below:

chr1 856020 . TGTGCTGTGTGTGTGT . 0 . END=856035;MOTIF=TG;NS=3;REF=8;RL=16;RU=TG;VT=STR GT:ALLREADS:AML:DISTENDS:DP:DPA:GB:PL:PQ:Q:SB:STITCH 0/0:0|1:1/1:45:1:1:0/0:0:inf:1:5:1 0/0:0|1:1/1:-56:1:1:0/0:0:inf:1:5:1 0/0:0|1:1/1:-14:1:1:0/0:0:inf:1:5:1

There is a dot on the ALT column and the GT is '0/0' across all samples. What do these mean?

Best,

Emma

[Melissa Gymrek]

Hi Emma,

This means there were no alternate alleles found, so every sample is homozygous for the reference allele (0).

~Melissa

--
You received this message because you are subscribed to the Google Groups "lobSTR user group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to lobstr-user-group+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.