ask help for CNVnator genotype

Question

[xiachujing]

I used the following commands to get genotypes,

./cnvnator -root sample.root -genome hg19 -chrom chr1 -unique -tree chr1.bam ./cnvnator -root sample.root -genome hg19 -chrom chr1 -d ./b37 -his 100 ./cnvnator -root sample.root -chrom chr1 -stat 100 ./cnvnator -root sample.root -chrom chr1 -partition 100 ./cnvnator -root sample.root -d ./b37 -genotype 100

For the step5, when appeared ">", I typed "chr1:1-1000", then the output is Can't find directory 'bin_1000'. Can't find directory 'bin_1000'. Genotype chr1:1-1000 sample.root -1 -1

Why the copy number of my data is "-1" ? I tried lots of data, all outputs are the same. I can use the sample.root to call CNV sucessfully.

Thanks.

Answer 1

[cyrielle]

A Docker container for human CNV calling with CNVnator was recently developed. All you need to do is download the container and and make sure you have a WGS .bam. Calling then starts automatically, so no need to compile and run the software yourself. More info is available in this blogpost goo.gl/uodlUO