Why did Bedtools intersect output a zero byte file
Hey everyone, So I am trying to use bed file for intersection with my vcf file. The command appears to execute but out-put a zero byte file each time. Does this mean the files do not match?or it didn't output properly? or something wrong with my command. Could you help please? the command is bellow.
bedtools intersect -a a.bed -b b.vcf -wa > intersect.txt
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Most likely, either your BED or VCF file does not have the 'chr' prefix for the contig names
@Alex already answered this in other thread: C: Bedtools intersect error
Check your identifiers in both files to begin with.
Sorry for late response. Biostar won't allow me post more than 5 times. But thanks, I think there is no match in my genomic region.
No problem. That limit will go away as you participate more on the site.
If there are no matches between the files, then yes, bedtools intersect will generate no output, resulting in your size 0 file.
Edit: blargh, too late, that's what I get for prioritizing my job over answering Biostar questions... ><;