Question: Why did Bedtools intersect output a zero byte file
0
gravatar for jaqx008
2.2 years ago by
jaqx00870
jaqx00870 wrote:

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

variant calling vcf bedtools • 861 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by jaqx00870
1

@Alex already answered this in other thread: C: Bedtools intersect error

Check your identifiers in both files to begin with.

ADD REPLYlink written 2.2 years ago by genomax83k

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.

ADD REPLYlink written 2.2 years ago by jaqx00870
1

No problem. That limit will go away as you participate more on the site.

ADD REPLYlink written 2.2 years ago by genomax83k

Most likely, either your BED or VCF file does not have the 'chr' prefix for the contig names

ADD REPLYlink written 2.2 years ago by Kevin Blighe59k

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... ><;

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by cschu1812.3k
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