What does ALT[0] mean?

Question

[Emms]

Hi, all. I'm studying WES analysis for new project and I have a questions, please help. I'm working in a wet lab, so it's no different from a blank paper.

I wanna know that (variant.ALT[0] != ""). It was one of many filter conditions. What does ALT[0] mean in INFO.field? According to the manual, "" means deletion, is that right? Or is there something else?

Thank you.

Answer 1

[Pierre Lindenbaum]

ALT[0] is the first ALTernate allele of the variant.

[Emms]

thanks for reply. but I still don't understand. could you please explain in more detail?

[cmdcolin]

in a VCF, the "ALT" column can contain multiple entries. this would indicate that there are different "alternative alleles" observed in your data at that position. for example, the reference genome might say G, and in your data you saw that there was also a C and a T observed at that position, so the ALT column would be C,T (comma separated list). you might ask why multiple things could occur at that position, but some reasons include e.g. a human is diploid so even a single person might have two different alternatives at that position, but also, a VCF can contain the data of more than one person in it

[Emms]

thank you guys. you means "multiallelic" right? I can study the next step!