Dear all, I am trying to use CNVkit to detect copy number variant in my samples. My sequencing data is derived from peripheral blood so I am looking for germline copy number variants. I don't have tumor sample, only germline.
I followed the suggestions of the documentation and here is the flow of the pipeline that I used to analyse my data:
python3 /usr/local/cluster/bin/cnvkit.py batch germline_sample.bam --n --targets brca_slop.bed --fasta hg19.fa --output-reference germline_sample.cnn --output-dir cnvkit_brca/
python3 /usr/local/cluster/bin/cnvkit.py segmetrics -s germline_sample.cn{s,r} --ci
python3 /usr/local/cluster/bin/cnvkit.py call germline_sample.segmetrics.cns --filter ci -o germline_sample.calls.cns
As test I used a sample that I know has a deletion of the exon 23 in BRCA1 gene. But I did not found any result:
python3 /usr/local/cluster/bin/cnvkit.py breaks germline_sample.cnr germline_sample.calls.cns
Found 0 gene breakpoints
gene chromosome location change probes_left probes_right
python3 /usr/local/cluster/bin/cnvkit.py gainloss germline_sample.cnr -s germline_sample.calls.cns
*WARNING* No chrX found in probes; check the input
Treating sample gremline_sample as male
*WARNING* No chrX found in probes; check the input
*WARNING* No chrX found in probes; check the input
*WARNING* No chrX found in probes; check the input
Found 2 gene-level gains and losses
gene chromosome start end log2 depth weight cn probes
BRCA2 chr13 32890547 32972958 -0.243229 418.202 36.7767 2 269
BRCA1 chr17 41197644 41276164 -0.795891 284.416 22.3257 1 309
Definitely I am missing something. Is my flow correct? Can someone help me in understand what is wrong and how I have to use CNVkit on my data? Thanks for the help.
Stefania