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lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation
GNU General Public License v3.0
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Invalid record in file : BED format #256

Open v-lakhujani opened 1 month ago

v-lakhujani commented 1 month ago

I am getting invalid record error

This is annotsv v3.3.6

-- genesAnnotation --
bedtools intersect -sorted -a 20240910001-1.sv.NA.formatted.sorted.bed -b /opt/AnnotSV/share/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed -wa -wb > 20240910001-1/20240910001-1.sv.annotated.cnv.final.bed.tsv.tmp.tmp
Error: Invalid record in file 20240910001-1.sv.NA.formatted.sorted.bed. Record is 
1   2192220 0   BND Sniffles2.BND.952S0 N   [2:85179275[N   60.0    PASS    .   1.0000000   2   .   0.0,0.0,2.0,2.0,2.0 False   False   .   .   True    .   .   3.536   +-  2.  .   .   .   SAMPLE  0   2   5   .   1/1 NA
Exit with error

is it because if [2:85179275[N ?

lgmgeo commented 1 month ago

No, this is because of the start and end positions: chrom = 1 start = 2192220 end = 0 This is not a valid BND localisation.