Dear all,
we do have a large number of VCF files , I am attempting to merge all of them by using VCF tools, in the following way :
for f in *.vcf do bgzip -c "$f" > "$f.gz" tabix -p vcf "$f.gz" done
and :
vcf-merge *vcf.gz.
However, during the vcf-merge step, I am getting an error :
Use of uninitialized value in hash element at /usr/local/share/perl/5.18.2/Vcf.pm line 1720, <__ANONIO__> line 1158. Use of uninitialized value in hash element at /usr/local/share/perl/5.18.2/Vcf.pm line 1720, <__ANONIO__> line 1158.
any advice on why we do get this error ? many thanks !
-- bogdan
you could try vcflib's merger.
Thank you Ram for your suggestion, a simple question though : as echo prints the command; how do I execute the java command that echo will print :
"echo -n "java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta -o combined_output.vcf -genotypemergeOptions UNIQUIFY " && for vcf_file in $(ls folderWith100VcfFiles/*.vcf); do echo -n "--variant ${vcf_file}"; done"
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