multiplicity of a variant

[SebastianHollizeck]

Hi,

thanks a lot for developing this, it looks exactly like something I want to use.

I am slightly unsure what to do for the multiplicity and variant counts

Your example data shows multiplicity of 2 for some variants, but i dont understand how to replicate that with my data

for example, if I have 3 variants present in multiple samples in different amounts e.g.

Sample	A>C	A>G	A>T
1	5	10	0
2	0	10	0
3	5	5	5

would that lead to multiplicity

Sample1	Sample 2	sample 3
3	3	3

or

Sample1	Sample 2	sample 3
2	1	3

And for the counts, do I make a new line for each of the variants, or do they get summed up?

so y being

Sample1	Sample 2	sample 3
5	0	5
10	10	5
0	0	5

or

Sample1	Sample 2	sample 3
15	25	15

I would love to use this tool i just want to make sure I use it correctly.

Thanks, Sebastian

[llyzhng]

Hi Sebastian,

The multiplicity is the number of alleles on which a variant is present, so each variant will have its own value and it may different among samples. Multiplicity will always be less than or equal to the total copy number at the locus.

The read count table should have a row for each variant.

[SebastianHollizeck]

Thank you for clearing that up, can you suggest a tool/method to estimate multiplicity of a variant? I have local copy number for each variant