vcf-merge problem

[diego diaz]

Hi all

I am trying to merge several vcf files coming from the same genome. I am using vcftools, but the problem is that i am getting an empty output file.

First, I compressed all my sorted vcf files with bgzip

 for i in *.vcf; do bgzip $i; done

Then, I made the tabix index,

for i in *vcf.gz; do tabix -p vcf $i;done

Finally, I ran vcf-merge,

 ls /path/to/my/files/*vcf.gz | xargs ./vcf-merge > vcf_merged.vcf

but whe I checked the vcf_merged.vcf file, it was empty. I tested the tbi files too, with -l flag, to list the chromosomes,

 tabix -l part_1.vcf.gz

and the chromosmes were OK. Then I tried to make a query

tabix part_1.vcf.gz CM003281.1:1,20276829; but I got nothing.

The only thing I can think is wrong is the name of the chomosomes, they have a dot at the end. But I am not sure if this is a real problem.

Do you have any advise for this?

Thanks in advance!