Question: Why did Bedtools intersect output a zero byte file
0
gravatar for jaqx008
16 months ago by
jaqx00850
jaqx00850 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 • 521 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by jaqx00850
1

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

Check your identifiers in both files to begin with.

ADD REPLYlink written 16 months ago by genomax69k

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 16 months ago by jaqx00850
1

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

ADD REPLYlink written 16 months ago by genomax69k

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

ADD REPLYlink written 16 months ago by Kevin Blighe45k

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 16 months ago • written 16 months ago by cschu1811.7k
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