I received Whole Exome Sequencing data from an NGS company (CARIS, specifically). I received R1 and R2 FASTQ files, a BAM file aligned to hg38, and a VCF file.

I used CNVPytor to create a CNV plot (Manhattan plot), by following this example Jupyter Notebook here: https://github.com/abyzovlab/CNVpytor/blob/master/examples/PythonLibraryGuide.ipynb

However, when I run this code on my data, I get the following graph:


Furthermore, I tried to use CNVKit and used the following steps/code:

cnvkit.py batch TN21-116928.DNA.bam --normal -m hybrid --fasta hg38.fa --targets targets.bed --output-reference my_reference.cnn

Where "targets.bed" was a file of the following form:

chr1    33306766    33321098    A3GALT2
chr22   42692121    42721298    A4GALT
chr3    138123713   138132390   A4GNT
chr12   53307456    53324864    AAAS
chr12   125065434   125143333   AACS
chr3    151814073   151828488   AADAC

The graph created from this is the following: Graph 2

Does anyone know where I am going wrong? Any pointers?

  • 1
    $\begingroup$ cnvkit.py scatter -s Sample.cn{s,r} -c chr7 maybe? Anyway its a cool question (except for the results) $\endgroup$
    – M__
    Aug 15 at 16:26


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