Duplicate SV IDs with identical chrom/start/end positions in AnnotSV TSV output

[poddarharsh15]

Hi, @lgmgeo

Thank you for developing and maintaining AnnotSV—it’s an excellent tool for structural variant annotation. However, I encountered an issue while processing my data.

After running AnnotSV, the resulting .tsv file contains a large number of SVs with the same ID and identical chromosome start and end positions. I’m not sure why this duplication occurs, as I expected each SV to be uniquely identified in the output.

Could you please help clarify why this is happening? I’ve attached the TSV file and the exact command/code I used for reference.

AnnotSV -annotationsDir ${ANNOTSV_DIR} \
        -annotationMode both \
        -includeCI 0 \
        -overlap 100 \
        -overwrite 1 \
	-hpo HP:0001561,HP:0001276,HP:0002371,HP:0025313,HP:0033725,HP:0002197 \
        -genomeBuild GRCh38 \
        -tx ENSEMBL \
        -SVinputfile ${INPUT_VCF} \
        -outputFile ${OUTPUT_VCF} \
        -outputDir ${OUTPUT_DIR} \
	-variantconvertDir /home/tigem/h.poddar/structural_varinats/variantconvert \
	-vcf 1

BA013_P_1.zip

[lgmgeo]

Please, look at the README.

Full and split lines:

• Annotation on the “full” length of the SV. Every SV are reported, even those not covering a gene. This type
  of annotation gives an estimate of the SV itself.
• Annotation of the SV “split” by gene. This type of annotation gives an opportunity to focus on each gene
  overlapped by the SV. Thus, when a SV spans over several genes, the output will contain as many annotations lines as genes covered. This latter annotation is extremely powerful to shorten the identification of mutation implicated in a specific gene.