CoordinatesOutOfBoundsException: Contig bounds errors

[poddarharsh15]

Hi @julesjacobsen,
I am encountering an error related to contig bounds. I have attached a text file with all the details. Could you kindly have a look and let me know how best to resolve this issue? Thank you very much for your support.[I am working with ref_genome hg38, VCF called on GRCh38]

org.monarchinitiative.svart.CoordinatesOutOfBoundsException: One-based coordinates HSCHRUN_RANDOM_128:92984-92984 out of contig bounds [1,92983]

exomiser.txt

[julesjacobsen]

The error is being caused by those variants being placed past the last base of the contig. It might be the caller you used which is causing this? Can you include the VCF lines for those failing variants and the VCF header? You can email me if you can't share that here.

[poddarharsh15]

Hi @julesjacobsen

Here is the variant info and vcf file information in a excel file.

chrUn_KI270435v1	92984	667974	N	CGGAGTGGGGTGGAATGGAATCAACGCGAGTGCAGGGGAATGGAA	.	PASS	SVMETHOD=DYSGUv1.8.3;SVTYPE=INS;END=92984;CHR2=chrUn_KI270435v1;GRP=667974;NGRP=1;CT=3to5;CIPOS95=0;CIEND95=0;SVLEN=45;KIND=extra-regional;GC=46.85;NEXP=10;STRIDE=5;EXPSEQ=ggaatggaaT;RPOLY=90;OL=0;SU=54;WR=0;PE=0;SR=0;SC=54;BND=10;LPREC=0;RT=pe	GT:GQ:PSET:HP:AF:MAPQP:MAPQS:SU:WR:PE:SR:SC:BND:NMB:COV:NEIGH10:PS:MS:RMS:RED:BCC:FCC:ICN:OCN:PROB	1/1:190:-1:0:0.19:37.4:0.0:54:0:0:0:54:10:0.0:53.17:1:26:28:0:0:0:0.0:3.607:0.0:0.592

exomiser_variant.xls