Beedtools intersect unable to open a vcf file
What could be the reasons Bedtools return this error message
error unable to open file exiting
I am developing an application that uses intersect in the research env. of Genomics England. The VCF files all have an acceptable format. However, with some of them, bedtools doesn't like them. Any clue where to start debugging?
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what did you try ?
Hi! Maybe is a good idea to specify the exact command you are using to run bedtools so that you can get better help. Having said this, usually this kind of error comes from bad formatted files, maybe you can make sure that all the files are tab separated? Also there are many posts already out there related with this error, f.e. this, and many more in github, maybe you can have some idea of the issue going through them :).