Hi everyone,

I have to genotype a particular deletion (chr6:149762615–149763234) and I am using Delly for that. So, basically I am not using Delly in the discovery mode where you screen the whole genome to find and genotype structural variants, instead I am using it to genotype a specific known deletion. I am not clear about the exact type of file format in which I can input my known deletion. I wasn’t able to find it on this github page (https://github.com/dellytools/delly), so I am following the ChatGPT guide.

I used the following file (known_deletions.vcf) to input my deletion of interest to Delly:

##fileformat=VCFv4.2
##ALT=<ID=DEL,Description="Deletion">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variant">
##contig=<ID=chr6>
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
 chr6    149762615       del_chr6_149762615_149763234    N       <DEL>   .       PASS    SVTYPE=DEL;END=149763234;SVLEN=-620

I ran delly using this command-line:

delly call -g hs1.fa -v known_deletions.vcf -o sample_output.bcf Adygei.HGDP01381.cram

and it gives me this error:

Error: Delly genotyping requires local SV assembly (INFO/CONSENSUS) and breakpoint (INFO/CONSBP) introduced in delly v1.1.7!

If someone can please guide me how to run delly to genotype a specific deletion, particularly how to prepare the input file for deletion.

If someone knows other programs (other than delly) to genotype a known deletion and which are easy to install and use, and if someone has any useful script for that, please suggest.

Thank you