Default CNV call thresholds for haplotype chromosome s

Question

[enes]

Hi, I confuse a topic that about the CNV call. The default thresholds are -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 for discrete copy number. But these thresholds doesn't work for chrY and chrX. What is the gender chromosomes default thresholds?

Thanks

[German.M.Demidov]

It depends if your sample is from a male or from a female and whether you work within the PAR region.

[enes]

Actually I wonder the male because female chromosomes are diploid. The problem is about haploid chromosomes. So if you know the default male thresholds, please notify me. Thank you

[German.M.Demidov]

is it germline calling? cnv-kit works best for somatic

are control samples males or females?

[enes]

Does matter the germline or somatic for haplotype gender chromosome thresholds?

Can't be reference samples female and male mixed? Let say all reference samples come from male, what are the thresholds?

[German.M.Demidov]

Somatic (cancer) CNVs usually have to be called not in 100% of the cells since we sequence tumor and normal cells (immune/stroma) in bulk

Can't be reference samples female and male mixed?

The copy-number status is usually defined from a log-ratio between normalized coverage in test and control samples. Thus, for chrX it is expected to be log(½) for males and log(2/2) for females - if our control samples are females.

E.g. if your control samples are males and you have copy-number 2 of some gene on Y chromosome, you'd expect it to be log(2/1) - so for the threshold you need to choose something between log(1/1) and log(2/1). I'd say log(1.5/1) would be a good threshold, which is around 0.4.

[enes]

when I add thresholds for calling step, I used this code:

cnvkit.py call {snakemake.input.cns_file} -m threshold -t=-2,-0.4150375,0.3219281,0.8073549,1.169925 -o {snakemake.output.cns_call}) {log}

How can I specify thresholds for gender chromosomes?

[German.M.Demidov]

simply put them after -t parameter!

[enes]

Actually this is what I did. -t=-2,-0.4150375,0.3219281,0.8073549,1.169925

-t parameter is working for each chromosomes including chr1 to chr22. My question is how can I put thresholds for gender chromosomes(chrX,chrY)?

[German.M.Demidov]

like, -t=-2,0.4,1 - I think 1 is when chrY is tripled (or chrX in males is triplicated which would be a female of course)

[enes]

Nope, when you use -t=-2,0.4,1 like that,

• it means -2 and less will assign CN=0
• -2 and 0.4 range CN=1
• 0.4 and 1 range CN= 2 and etc.

These theresholds are used for chr1 to chr22. Am I wrong?

[German.M.Demidov]

yes, they are used for your whole dataset

you call CNVs twice

then you manually merge results from chrX and chrY in males and the rest that you got with your other thresholds

[enes]

nope, they are used for only somatic chromosomes. In male, probably there is another threshold for haplotype chromosomes (sex chromosomes, x and y).

What is these default thresholds? that is my main question..

[German.M.Demidov]

I know which thresholds have to be used because I've wrote my own tool for CNV detection ( https://github.com/imgag/ClinCNV ) - I simply don't understand what is going one here, what are somatic chromosomes (sex chromosomes?), another thresholds for haplotype choromosomes is depending on whether your control sampels are males or females (because it is log2 (coverage of case / coverage of control) ) - I don't really get the question, sorry