[Vcftools-help] vcf-isec: tabix index may be broken?

[Mallott, J. <Mal...@pe...>]

Hi, I'm trying to run vcf-isec, but I am getting some weird outcomes and a vague error message. I'm sorry I don't have something more specific. Here is the end of the output when I try running vcf-isec. I have no idea what this means or what I could be doing wrong.

##reference=file:///scratch/tcs/tcs/db/resources/human_g1k_v37.fasta
##source_20120302.1=/Users/jacobmallott/Desktop/Tools/vcftools_0.1.7/bin/vcf-isec -c Analysis_3-28-2012/patient7andmother1.vcf.gz Exome4_4-2-2012.recode.vcf.gz
##sourceFiles_20120302.1=0:Analysis_3-28-2012/patient7andmother1.vcf.gz,1:Exome4_4-2-2012.recode.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT X
Warning: Read 0 lines from Analysis_3-28-2012/patient7andmother1.vcf.gz, the tabix index may be broken.
 at /Users/jacobmallott/Desktop/Tools/vcftools_0.1.7/bin/vcf-isec line 21
main::error('Warning: Read 0 lines from Analysis_3-28-2012/patient7andmoth...') called at /Users/jacobmallott/Desktop/Tools/vcftools_0.1.7/bin/vcf-isec line 89
main::__ANON__('Warning: Read 0 lines from Analysis_3-28-2012/patient7andmoth...') called at /Users/jacobmallott/Desktop/Tools/vcftools_0.1.7/bin/vcf-isec line 274
main::vcf_isec('HASH(0x7ff392028908)') called at /Users/jacobmallott/Desktop/Tools/vcftools_0.1.7/bin/vcf-isec line 12