Query Regarding "Varscan2Cns" Output

Question

[subhi.2k7]

I have a very specific query regarding the output we get after running "varscan2cns" in Varscan2. The output has entries as given below, which are difficult to interpret.

There are some examples below of the output I got:

What do the " * " , " + " and " - " suggest?

*/+G, -C/-C, */-AAGGGGCCGGAA, */-GG

Answer 1

[Fabio Marroni]

For what I can remember (It's a while since I last used varscan):

*/+G: One allele is like the reference, the other one has an insertion of a G

-C/-C: Both alleles have a deletion of a C

*/-AAGGGGCCGGAA: Heterozygous deletion of AAGGGGCCGGAA

*/-GG: Heterozygous deletion of GG.

[subhi.2k7]

thanks Fabio!!

but I was thinking how can you have heterozygous deletion of AAGGGGCCGGAA for a single position??