CNV calling

[phdstudent-oje]

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.

[tobiasrausch]

Yes, please use CN or RDCN. The long answer is:

For copy-number variants delly is currently not using the GT field because that's commonly used for hom. ALT (1/1), het. (0/1) and hom. REF (0/0). For copy-number variants I do not know the allelic distribution. For instance if the total copy-number of a segment is 8 the allelic copy-numbers could be 4 and 4, or 8 and 0, or 1 and 7, ...

Because of that issue delly only outputs the total copy-number in FORMAT:CN and the copy-number likelihoods for each copy-number state (FORMAT:CNL).

[phdstudent-oje]

Dear @tobiasrausch,

Hi I'm Oh.

Thanks for your reply.

Have a nice day!

Oh.