search

nf-core / variantbenchmarking

A nextflow variant benchmarking pipeline - premature
https://nf-co.re/variantbenchmarking
MIT License
6 stars 6 forks source link

wittyer bug #59

Open kubranarci opened 1 week ago

kubranarci commented 1 week ago

Description of the bug

Wittyer raises exceptions for specific kind of BND

relates to this: https://github.com/Illumina/witty.er/issues/9

Command used and terminal output

from svaba:
System.IO.InvalidDataException: Found a symbolic SV have no END or SVLEN key in info field, cannot process the variant 
  7     152075573       4168826:2       A       A[21:11079623[  0       PASS    MATEID=4168826:1;NM=-1;SPAN=-1;MATENM=-1;IMPRECISE;DISC_MAPQ=55;AN=2;MAPQ=55;AC=0;EVDNC=DSCRD;SVTYPE=BND;NUMPARTS=0;SCTG=7:152075573(+)-21:11079623(-)__21_11074001_11099001D   GT:AD:DP:GQ:PL:SR:DR:LR:LO
ex

from delly:
System.ArgumentException: Invalid interval given: Start(142535829) and Stop(10086436)

Relevant files

No response

System information

No response

kubranarci commented 1 week ago

sam error for lumpy as well:

Found a symbolic SV have no END or SVLEN key in info field, cannot process the variant