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
1 answer
GATK also has one that i've used recently for thousands of vcfs.
There will be someone that recommends make here, but I'm not good at that, so I'd say generate the GATK command with a bunch of echos. Something like:
# Newlines added for readability - remove newlines before you run the command
$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;
This will echo the static part first and echo, for each vcf file in the directory folderWith100VcfFiles, a properly formatted --variant argument.
Thanks Ram for keeping the conversation organized. To reiterate my previous question about how do I execute the java command that echo will only 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"
use a list:
find path -type f -name "*.vcf" > input.list
and then use GATK with --variant input.list
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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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