Question: Bedtools intersect error
0
gravatar for Inquisitive8995
18 months ago by
Inquisitive8995170 wrote:

Hi, I am trying to use bedtools intersect to intersect between a vcf and a bed file. My command is this

bedtools intersect -header -u -a ABC.vcf -b XYZ.bed > check.vcf

My bed file looks like this

chr6    29000001        33000000

But everytime I try this. It gives me the following error:

Error: Invalid record in file ABC.vcf. Record is  
chr6        60002        .        A        <*>        0        .        DP=5;I16=5,0,0,0,191,7301,0,0,208,8656,0,0,47,495,0,0;QS=1,0;MQ0F=0     PL  0,15,104

I tried to remove this particular position and redo. But it gives error for the next position. What could be the issue here ? Any help would be appreciated.

sequence vcf software error • 664 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by Inquisitive8995170

Can you first check if all the file formats you are using are OK for input to bedtools? Perhaps it's the <*> that is causing problems?

ADD REPLYlink written 18 months ago by lieven.sterck8.5k

Yes, I have rechecked all the file formats from the original sam file to the final input vcf file. Those seem to be fine

ADD REPLYlink written 18 months ago by Inquisitive8995170

I'm far from an expert here but I don't see the <*> as a valid option in the vcf file format . Did you try removing/altering this

ADD REPLYlink written 18 months ago by lieven.sterck8.5k

It is mentioned in one of the posts that <*> refers to alternate allele or homozygous reference sites.
What does <*> mean in a vcf file?

ADD REPLYlink written 18 months ago by Inquisitive8995170
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