Question: Problem with vcf-merge
gravatar for vncnt.anna
9 months ago by
vncnt.anna0 wrote:

Hi I am trying to merge two VCFs which I got from using platypus joint variant calling on bam files which I had to split from the original files I got, they were just to big for the cluster I'm using and had to split them per chromosome for variant calling.

I did zip my vcfs using bgzip and then indexed them with tabix :

bgzip -c file1.vcf > file1.gz

tabix -p vcf file1.gz

and then when I run vcf merge file1.vcf file2.vcf > merged.vcf, I get the following error few seconds after submitting the job(see below for command line):

Use of qw(...) as parentheses is deprecated at /com/extra/vcftools/0.1.9/lib/perl5/site_perl// line 1622.
[main] fail to load the index file.
The command "tabix -l /home/annavct/Klinefelter/faststorage/people/anna/04_variants_split/variants_Y.vcf" exited with an error. Is the file tabix indexed?
 at /com/extra/vcftools/0.1.9/lib/perl5/site_perl// line 177.
        Vcf::throw('Vcf4_0=HASH(0x1876428)', 'The command "tabix -l /home/annavct/Klinefelter/faststorage/p...') called at /com/extra/vcftools/0.1.9/lib/perl5/site_perl// line 2599
        VcfReader::get_chromosomes('Vcf4_0=HASH(0x1876428)') called at /com/extra/vcftools/0.1.9/bin/vcf-merge line 182
        main::init_cols('HASH(0x1866118)', 'Vcf4_1=HASH(0x1872f90)') called at /com/extra/vcftools/0.1.9/bin/vcf-merge line 264
        main::merge_vcf_files('HASH(0x1866118)') called at /com/extra/vcftools/0.1.9/bin/vcf-merge line 12


snp next-gen • 271 views
ADD COMMENTlink modified 9 months ago by ATpoint21k • written 9 months ago by vncnt.anna0
gravatar for ATpoint
9 months ago by
ATpoint21k wrote:

You have to use vcf-merge on the gzipped and tabixed files directly. In your command you use them on the uncompressed ones:

bgzip file1.vcf > file1.vcf.gz
tabix -p file1.vcf.gz
vcf-merge file1.vcf.gz file2.vcf.gz > merged.vcf
ADD COMMENTlink written 9 months ago by ATpoint21k
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