I don't know where you got your second sentence -- let's call them (1) and (2), OK?
As pointed out, (2) is ungrammatical as a question, so let's mark it with an asterisk "*".
How can you go to your sister's house this afternoon?
*How you can go to your sister's house this afternoon?
That is, sentence (2) is wrong in standard English; you shouldn't use it. That answers your question.
More than that, however, it means that if anyone taught you to ask a question that way, they were wrong as far as standard English is concerned; and that anybody around you that would ask an English question like (2) is doing it wrong for standard English.
This kind of question may well be common, however, in the English spoken by people around you, especially if they are not native English speakers, or if there is a distinctive local English dialect, like Indian English.
The reason for the confusion, I think, is that (3) (which is (2) without the question mark or capital),
- how you can go to your sister's house this afternoon
does occur grammatically in standard English. But not as a question, only as a complement clause;
- I don't know how you can go to your sister's house this afternoon; we're not done.
in this case how you can go to your sister's house this afternoon is an embedded question complement clause that's the direct object of I don't know.
The big difference between a real question that should take a question mark and should start with a capital letter is that real questions invert the subject and the auxiliary verb (and if there isn't an auxiliary verb, invert do) like (1), while embedded question subordinate clauses don't invert them (and therefore don't use do) like (3). (2) is ungrammatical only because it's used as a question.