Dear all,
i tried to use estimated purity to adjust the allele specific copy number output from cnvkit, but it would generate minus copy number integer value.
below is my command.
cnvkit.py call sample.cns -v sample.vcf --purity 0.39 -m clonal -o sample_purity.call.cns
below is the output .cns file with minus integer copy number value
chromosome start end gene log2 baf cn cn1 cn2 depth probes weight
2 236578628 237490302 AGAP1,GBX2,ASB18,IQCA1,ACKR3 -9.96578 0.00387202 -1 0 -1 26.4653 99 49.9862
did i use cnvkit in wrong way?
thanks.
•
written
by
xiaoqiaoliu •
It just indicates loss in the sample, i.e., deletion, as evidenced also by the log2 and baf (B allele frequency) values.
The CNVkit manual states that, when cn1 and cn2 differ, it is indicative of allelic imbalance:
Allelic imbalance, including copy-number-neutral loss of heterozygosity (LOH), is then apparent when a segment’s “cn1” and “cn2” fields have different values.
[source: http://cnvkit.readthedocs.io/en/stable/pipeline.html]
There are many copy number programs out there that say that they can detect LOH, allelic imbalance, etc., and none of these has ever made its way to be a clear winner. So, we have many groups using many different programs. Thankfully, one output format has more or less becomes standardised, which is generally referred to as CN segment data:
sample chr start end num_probes segment_mean / log2_ratio
You have this data, which is good.
I would not use the cn1 and cn2 values for downstream analyses.
Kevin
however, how can i get absolute copy number and LOH status for these segment with minus cn?
You can output the absolute copy number with the call command.
In this case, it looks like the region is entirely deleted in tumour, i.e., no copies. The BAF is virtually nil / zero, which, coupled with the log2 ratio, implies complete deletion.
log2 of -9.96578 is equivalent to a tumour-to-normal ratio of:
2^(-9.96578) = 0.00100000296
thanks for the reminding, Eric. i use v0.8.5. i should update to 0.9.3.
Hi, Eric. I also use estimated purity to adjust integer values. but the cn1 I got -3 and cn2 got 0, what it means? Can I see it as LOH region?
Log in to answer this question.
Hi, there. I also use estimated purity to adjust integer values. but the cn1 I got -3 and cn2 got 0, what it means? Can I see it as LOH region?