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CombineVariants Genomestrip

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

Hi,

I've generated vcfs for deletions, genotyped with genomestrip, multiple indivuals/samples, for each of six chromosomes, and I'd like to combine them. The problem is that:

. /etc/profile.d/modules.sh
module load jre/1.7.0_25
module load gatk/3.4-0

GenomeAnalysisTK -R ${refseq} \
-T CombineVariants --genotypemergeoption UNSORTED \
-V ${vcf}.chr2L.vcf \
-V ${vcf}.chr2R.vcf \
-V ${vcf}.chr3L.vcf \
-V ${vcf}.chr3R.vcf \
-V ${vcf}.chrX.vcf \
-V ${vcf}.chr4.vcf \
    -o unfilt.${vcf}.vcf

returns ....

ERROR stack trace 
java.lang.IllegalStateException: Key CNF found in VariantContext field FORMAT at chr2L:16495 but this key isn't defined in the VCFHeader.
ERROR MESSAGE: Key CNF found in VariantContext field FORMAT at chr2L:16495 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.

In the input vcfs, the CNF key in the VariantContext field FORMAT is shown here:

GT:CNF:FT:GL:GP:GQ      0/0:1.9552:PASS:-0.00,-7.56,-194.96:-0.00,-9.62,-198.31:96 

So I guess I have to edit the vcf header include some indication of the CNF field.. does that sound correct ?

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