Merge CNVnator output of multiple samples

Question

[zhang248]

I am using CNVnator for multiple samples. I get a output of each individual, now I want to merge them, if anyone knows how to do or what tool can make this.

[guillaume.rbt]

I had the same problem and I haven't found any available tool to merge output from CNVnator...

I eventually used delly2 to find structural variants, because it handles multi-sample calling.

[zhang248]

Sorry for replying to you so late. I just try delly2 and it seems to be very slow with command "delly call -t DEL -g $GENOME -o s1.bcf $BAM1 $BAM2 ......". So, I think I just can use "delly call -t DEL -g $GENOME -o s1.bcf $BAM1" separately and then merge them with "delly merge". Am I right?

[guillaume.rbt]

Yes it's better to merge after, this is the pipeline I use (from the documentation on the github)

1. delly call on each bam :

   delly call -t DEL -g your_genome.fa -o first_calling_1.bcf your_bam_1.bam

   delly call -t DEL -g your_genome.fa -o first_calling_2.bcf your_bam_2.bam

2. merge all results :

   delly merge -t DEL -o first_merge.bcf first_calling_1.bcf first_calling_2.bcf

3. re-genotyping on all detected positions :

   delly/src/delly call -t DEL -g your_genome.fa -v first_merge.bcf -o second_calling_1.bcf your_bam_1.bam

   delly/src/delly call -t DEL -g your_genome.fa -v first_merge.bcf -o second_calling_2.bcf your_bam_2.bam

4. merge with bcftools

   bcftools merge -m id -O b -o final_merge.bcf second_calling_1.bcf second_calling_2.bcf

For the filters, I find that delly filter is too conservative, so I use my own filters (suppressing SVs with too much missing data, suppressing singletons...)

[zhang248]

Thank you very much, especially for you are the first person who answer my question among my all questions! I'll try it.

[guillaume.rbt]

 You're welcome ;)