Closed CodyS5 closed 5 years ago
Hi Cody,
Yes, that's correct. The second component (0|0) corresponds to the GB field, which indicates the length differences of the 2 alleles from the reference allele. In this case, allele 1 has the same length as the reference allele, but its sequence is different. You can verify that by looking at the ALT field for the corresponding VCF record
Best, Thomas
Hello,
I've been running HipSTR on a small dataset, and I'm a little confused by the output here. This is the output from a single locus, where the first individual has a 0/1 genotype, if I'm interpreting it correctly. Is the second part of this (0|0) supposed to indicate the difference in length between the genotype and the reference? I guess I'm unsure of how two different genotypes have the same length value here.
1:55388840 0|1:0|0:1.0:0.5:33:0:0:0:25.02|7.98:0|0:2.92:-2.48:31:-2.61:0|27:0|27:PASS 0|0:0|0:1.0:1.0:35:0:0:0:17.50|17.50:0|0:5.94:0.0:.:0.0:0|23:0|23:PASS 0|0:0|0:1.0:1.0:34:0:0:2:17.00|17.00:0|0:8.93:0.0:.:0.0:0|28:0|24:PASS
Thanks for any help you can offer!