Bedtools intersect error

Question

[Inquisitive8995]

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.

[lieven.sterck]

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?

[Inquisitive8995]

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

[lieven.sterck]

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

[Inquisitive8995]

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