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Query Regarding "Varscan2Cns" Output

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

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written by subhi.2k7 • subhi.2k7

2 answers

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.

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written by Fabio Marroni Fabio Marroni

thanks Fabio!!

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

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written by subhi.2k7 • subhi.2k7

thanks Fabio!!

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

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written by subhi.2k7 • subhi.2k7

Please delete this and move it to a comment on Fabio's answer. Also, it's a heterozygous deletion starting at that position, not just of a single position (it's a 12bp deletion, in fact).

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written by Devon Ryan Devon Ryan

Thanks....i dint realize that its a deletion starting from that base.. and thanks for correcting me...

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written by subhi.2k7 • subhi.2k7

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