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