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How to create gVCF file with VarDict

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Polina Bevad edited this page Jun 4, 2019 · 1 revision

The discussion about gVCF was in https://github.com/AstraZeneca-NGS/VarDictJava/issues/227.

For now, you can create gVCF file (genomic VCF, that will contain all the positions) with VarDict by using -p option.

Note: you have to use VarDict >= 1.6.0 from master branch or from release (when it will be created).

Some problems can occur with downstream scripts teststrandbias.R/testsomatic.R and var2vcf_valid.pl/var2vcf_paired.pl because the input after -p option is very huge (up to several dozen gigabytes).

To resolve this situation it is recommended to run VarDict separately for each chromosome and then process each var file to .R and .pl scripts, or use the scripts for autoprocessing of VarDict raw output like these: https://github.com/AstraZeneca-NGS/VarDict/tree/master/additions

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