Errors feeding bedtools subtract output into bedtools intersect

[leslie....@gmail.com]

Hello, 

I tried to feed in my output from bedtools subtract into bedtools intersect and depending on the version of bedtools I use I receive different errors (but the point is that it isn't working on either version of bedtools I tried!!). 

The error I received from bedtools version 2.24.0 was: ***** ERROR: illegal character '.' found in integer conversion of string ".". Exiting...

The error I received from bedtools version 2.21.0 was: unable to open file or unable to determine types for file bedtools_subtractAg.vcf (the file I created using bedtools subtract). 

I ran both tools using the default commands 

(bedtools subtract -a ./Ag.vcf -b ./B.vcf >> bedtools_subtractAg.vcf)

(bedtools intersect -a ./Ag_DNA.vcf -b ./bedtools_subtractAg.vcf >> Ag_RNADNA.vcf) 

Any idea as to why these errors are occurring? 

Thank you, 

Leslie

[Aaron Quinlan]

I think you might need to add the --header option to your first command such that the second command can recognize that the output of the first command is valid VCF.

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