delly2 outputs duplicate results?

[dodoflyy]

Hello, delly2 is giving me duplicate results like:

chr20   30422589        INV00028117     C       <INV>   429     PASS    PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN
chr20   30422589        INV00028117     C       <INV>   429     PASS    PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN
chr20   30422589        INV00028117     C       <INV>   429     PASS    PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN
chr20   30422589        INV00028117     C       <INV>   429     PASS    PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN

My commands:

delly2 call -g ${GRCh38} -x ${blacklist} -o ${delly2_dir}/${tumor_id}.raw.bcf ${bam_dir}/${tumor_id}_BQSR.bam ${bam_dir}/${normal_id}_BQSR.bam
  delly2 filter -f somatic -s ${samples} -a 0.1 -o ${delly2_dir}/${tumor_id}.pre.bcf ${delly2_dir}/${tumor_id}.raw.bcf
  delly2 call -g ${GRCh38} -x ${blacklist} -v ${delly2_dir}/${tumor_id}.raw.bcf -o ${delly2_dir}/${tumor_id}.geno.bcf ${bam_dir}/${tumor_id}_BQSR.bam ${control_bams}
  delly2 filter -f somatic -s ${samples} -a 0.1 -o ${delly2_dir}/${tumor_id}.post.bcf --pass ${delly2_dir}/${tumor_id}.geno.bcf
  bcftools view -R ${autosomes} -O v -o ${delly2_dir}/${tumor_id}.filtered.vcf ${delly2_dir}/${tumor_id}.post.bcf

am I doing anything wrong?

[tobiasrausch]

For genotyping your candidate somatic SVs in a set of control genomes you need to use the output file from the pairwise somatic filtering, ${delly2_dir}/${tumor_id}.pre.bcf:

delly2 call -g ${GRCh38} -x ${blacklist} -v ${delly2_dir}/${tumor_id}.pre.bcf ... ${control_bams}