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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
MIT License
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Error getting unique VCF records from a two-VCF files comparison #368

Open splaisan opened 8 years ago

splaisan commented 8 years ago

( bedtools v2.25.0-70-g577fecf )

I try to intersect a vcf.gz with a vcf resulting from another bedtools subtract run run#1: bedtools intersect -a ${afile} -b ${bfile} > ${outfolder}/common_ab.vcf ; # runs OK run#2: subtract -a ${afile} -b ${outfolder}/common_ab.vcf

ERROR: Received illegal bin number 4294967295 from getBin call. ERROR: Unable to add record to tree.

Seems related to this Biostar post Thanks for help

PS: using the 2.25.0 stable version, similar commands trigger errors due to the absence of a VCF header in one or both input. Could this also be the trigger here? If yes, a readable error message would help.

arq5x commented 8 years ago

The best thing to do would be to use the -sorted option if possible.