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  • vcf-merge problem

    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

    Code:
     for i in *.vcf; do bgzip $i; done
    Then, I made the tabix index,

    Code:
    for i in *vcf.gz; do tabix -p vcf $i;done
    Finally, I ran vcf-merge,

    Code:
     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,

    Code:
     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!

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