ferracimo/gross

Graph-aware Retrieval of Selective Sweeps

gross's Issues

Can GRoSS be applied to polyploid data?

Hi Dr.Fernando
I found that "diploid data" is mentioned in your article.
Can GRoSS be applied to polyploid data?

Data conversion for format required for GRoSS

Hi, how the input data from Lazaridis et al. (2014) used is GRoSS paper, can be converted into vcf file or format required for GRoSS.

I downloaded the corresponding data from https://reich.hms.harvard.edu/datasets

The data is in PACKEDANCESTRYMAP format
.geno Genotype file
.ind Individual file
.snp SNP file

Thank you!

why some variants are filtered out in the final output?

my input number of variants is 1096103, but the output is only 189948 lines. Is that correct?
Thanks!

vcf file conversion

Is there a way to convert vcf files to the format required for the GRoSS package? Thank you!

graph file include the weighted migration events

Hi,

Can you give me an example of graph file that transformed from treemix results?

Thank you!

Dependence on Mailund's matchbox

Hi,
I supposed to use GRoSS, but am not able to install matchbox (which is in dependecies). Thomas Mailund says that he knows about the problem, but can't fix it now. Is there some way get around usage of mathbox?

Can we interpret significant gross result as "natural selection favored derived allele"?

HI,
I notice that the GROSS result is derived from chi statistics and is non-negative, thus I'm a bit puzzle about the direction of detected positive selection. For an SNP with a significant GROSS result, can we state that the derived allele of this SNP is favored by natural selection, and its frequency was elevating during the tested branch? Thanks for your help.