Few number of clonal and sub-clonal variants

[beginner984]

Hello

By 393472 SNPs for 17 samples, after running your software I am getting 600 clonal variants and 83 sub-clonal the rest are NA

Do you think something is going wrong with my data?

How it is possible from 393472 SNPs , less 1000 returns clonality information?
I look forward to hearing from you and thank you so much

[FunGeST]

Hi there,

Thanks for getting in touch.

Yes you probably should receive more clonality information than that you're right! Would you be able to provide some example data so I can look into it for you?

And regrading your logR issue here, setting logR arbitrarily to 1 should work fine.

Best wishes,
Benedict

[beginner984]

From heart thank you very much to answer me because I really need help

My variant caller has been Strelka and copy number caller SCAT

For LogR I have just put 1 for all

For tumour depth I put tumour ref counts +tumour var counts

I have attached my data sets here

https://www.dropbox.com/s/jq7ubwkiyn17dbn/My_data.RData?dl=0

Please have a look

I don't know if this does affect the results, but after producing variants and copy number data individually, by genomicrange R package I done intersection s that mutations be in the copy number segments

Thanks a million

[FunGeST]

Hi,

I can see that chromosomes in "CHROM" column of your cna_data object contain no "chr" prefix. This is an issue since Palimpsest uses these values to match with the vcf table, where the "CHROM" column does contain the "chr" prefix. You should add the "chr" prefix in cna_data and try again.
Also many lines are duplicated in your cna_data object.

Hope this helps,
Eric