bcftools call -v option

[prasundutta87]

Hi,

according to the help section of bcftools call, -v is variant sites only. I get both indels and SNVs with it.

When I don't use -v option, I do not get any result, as in no variants are discovered except a few indels. And all my GT field is 0/0. Could you please explain this difference?

[pd3]

Sorry, I don't understand the question. The -v option drops sites which have no alternate allele (ALT=.). That is the only difference.

[prasundutta87]

Thank you for the clarification.

[prasundutta87]

I believe I can close the issue on my own?