CNV calling

[oghzzang]

Dear @tobiasrausch,

Hi. I'm Oh.

I executed the delly for Germline CNV calling.

I want to ask about the genotype of my called CNVs (c1.cnv.bcf), or merge the calls (merged.bcf).

ref_fasta=${home_dir}/Reference/Homo_sapiens_assembly38.fasta
map_file=${home_dir}/Tools/delly/map/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz

### call CNV
delly cnv \
    -o c1.cnv.bcf \
    -g ${ref_fasta} \
    -m ${map_file} \
    ${sample_name}_recal.bam 

### Merge CNV into a unified site list
code not shown

### Genotype CNVs for each samples
code not shown

### Merge genotype using bcftools
bcftools merge -m id -O b -o merged.bcf c1.geno.bcf c2.geno.bcf ... c100.geno.bcf 

### Filter for germline CNVs
delly classify -f germline -o filtered.bcf merged.bcf

All genotype of CNVs is "./." as below.

As I know, "./." is non-call.

Anyway, I only have to use "RDCN", so does it matter?

Many thanks.

Oh.