I'm trying the dockerhub image with svtools and running as follows: <div class="sn

i found at least one of the offending lines: <div class="snippet-clipboard-content

bedpetovcf does not work with vcftobedpe output as input about svtools HOT 1 OPEN

anoronh4 commented on June 26, 2024

bedpetovcf does not work with vcftobedpe output as input

from svtools.

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anoronh4 commented on June 26, 2024

i found at least one of the offending lines:

##FILTER=<ID=svaba_LOWAS,Description="Alignment score of one end is less than 80% of contig length, or number of mismatch bases (NM) on one end is >= 10">

vcftobedpe turns this line into:

##FILTER=<ID=svaba_LOWAS,Description=""Alignment score of one end is less than 80% of contig length, or number of mismatch bases (NM) on one end is >">

and then this line becomes unparseable with with bedpetovcf. i found a few similar looking lines:

grep "\"\"" vcftobedpe.bedpe 
##FILTER=<ID=svaba_TOOSHORT,Description=""Contig alignment for part of this rearrangement has <">
##FILTER=<ID=svaba_LOWAS,Description=""Alignment score of one end is less than 80% of contig length, or number of mismatch bases (NM) on one end is >">
##FILTER=<ID=svaba_WEAKSUPPORTHIREP,Description=""Fewer then 7 split reads for variant with >">
##FORMAT=<ID=svaba_LR,Number=1,Type=Float,Description=""Log-odds that this variant is REF vs AF">

seems like strings are not well handled when special characters such as <>= are in the Description.

from svtools.

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