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Old 04-06-2012, 11:39 PM   #366
Junior Member
Location: Santa Cruz, CA, USA, Earth

Join Date: Apr 2012
Posts: 5
Default Concatenating vcf files

Hi y'all. I'm a retired old guy who spent his whole life wishing that genomics would come along, now it's here and I'm almost too old. But I have some data, a linux system, and some software running, and many problems/questions. Like the oldest dumbest grad student you ever hear of. Very gald to find this site.
Current question is how to concatenate vcf files for individual chromosomes into a single genome. Have been running vcf-concat (from vcf tools) but no matter what I try, get the same error messages.

The column names do not agree in [../Chrm2/Chrm2.vcf].
at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 32
main::error('The column names do not agree in [../Chrm2/Chrm2.vcf].\x{a}') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 114
main::concat('HASH(0x21cf518)') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 12

Yet as near as I can tell, the two .vcf files have exactly the same columns, nice illumina data, looks clean, something just not right. Thanks
AllanLindh is offline