Ask about chromosomal CNVs of a large number of chromosomes

nandeng1213nandeng1213 Los Angeles, CAMember


I'm using GATK to call CNVs. It works well for the cases of individual chromosomal CNVs as shown in the tutorial materials. But for the following case, which involves chromosomal CNVs of a large number of chromosomes, I'm wondering if it has overall shifted. I plot the copy ratio and MAF from ACNV procedure, it shows many chromosomes, for example, chromosome 2,4,5,6,7,12,16,17,19,20 (copy ratio close to 1) have MAF around 0.35, while deletion and amplification on other chromosomes are balanced (MAF = 0.5). It makes me a little bit confused, since in most of the cases, if no chromosome CNVs, the MAF should be around 0.5 (balanced); if there are CNVs, the MAF should be other values below 0.5 (unbalanced).

Please correct me if I understand wrong.



Best Answer


  • nandeng1213nandeng1213 Los Angeles, CAMember

    Hi slee,

    Thank you very much for answering my questions, it made me more clear now.

    I have another question. The first stage of CNV calling procedure, the tool calculates the percentage of coverage (POC) using the number of reads in a region divided by the total number of aligned reads. Then, based on the POCs to call CNVs. My question is, for example, we have two cases, one does not have any CNV along the genome, the total number of aligned reads are 100M; another one has 2X amplification on half of the chromosomes, the other half are copy-neutral. If the total number of aligned reads are still 100M, compare to the first case, for the second case, more reads would be gone to the amplification chromosomes, and less read would be on the copy-neutral chromosomes when we do the sequencing. In this case, would those copy-neutral chromosomes be detected as deletions?



  • sleeslee Member, Broadie, Dev ✭✭✭
    edited February 2017

    Hi @nandeng1213,

    In that case, we would expect two segments at copy ratios of 2/3 and 4/3. It is likely that these will be called as events by CallSegments (with the first being erroneously called as a deletion).

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