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//Vcf.pm 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//Vcf.pm 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//Vcf.pm 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