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[rmormando]

I am running CNVkit on some illumina reads but my output is a little strange. I am trying to look at the CNV coverage across the entire genome of S. cerevisiae.

My pipeline is as follows:

# align the raw short reads to the reference with minimap2
minimap2 -ax sr Saccharomyces_cerevisiae.fasta Sample_R1.fastq.gz Sample_R2.fastq.gz -o Sample.sam

# convert sam to bam and index
samtools sort Sample.sam -o Sample.bam
samtools index Sample.bam

# use the cnvkit pipeline to get read depth / coverage information and generate scatterplot
cnvkit.py target my_baits.bed -o my_targets.bed # my_baits.bed includes every chromosome from 0 to their full length (so no antitarget file is necessary)
cnvkit.py access Saccharomyces_cerevisiae.fasta -o access.bed
cnvkit.py reference -f Saccharomyces_cerevisiae.fasta -t my_targets.bed -o reference.cnn
cnvkit.py batch Sample.bam -r reference.cnn -d Sample_Out/
cnvkit.py scatter Sample.cnr -s Sample.cns -o Sample-scatter.pdf

And this is the scatterplot:

Sample-scatter.pdf

Can someone explain what this output gives me and how I can fix it so it shows every instance of copy number in a dispersed format (i.e., should show the dots behind the lines)?

[rmormando]

I dove a little deeper and got points in the VAF plot but I realized the tool is not picking up any probes in the data.

Loaded 56876 records; skipped: 0 somatic, 13486 depth
Kept 4284 heterozygous of 56876 VCF records
Showing 0 probes and 0 selected genes in region chrVIII
Wrote chrVIII-scatter2.pdf

How can this be? Sample_VCF-scatter.pdf