clinical-genomics-lund / aggregate_vcf

Script to aggregate vcfs from different callers

Aggregate VCFs

Requires vcf-module /data/bnf/scripts/CMD/vcf.pm

Execution

aggregate_vcf.pl --base BASE_VARIANT_CALLER [--freebayes/mutect/pindel/vardict/gatkhc/manta/strelka VCF [--fluffify-pindel] [--tumor-id --normal-id]
--base        Defines which variant caller is used as base vcf (required)

Any number of these are allowed, at least one required:
--freebayes VCF   Freebayes VCF path
--vardict VCF     VarDict VCF path
--mutect VCF      MuTect2 VCF path
--manta VCF       Manta VCF path
--pindel VCF      pindel VCF path
--strelka VCF     Strelka2 VCF path
--tnscope VCF     Tnscope VCF path
--gatkhc VCF      GATK HaplotypeCaller VCF path

Additional options:
--fluffify-pindel Modify pindel REF/ALT fields to be less than 1000 bp (comply with Manta).
--tumor-id STR    REQUIRED IFF STRELKA: Sample ID for for tumor sample
--normal-id STR   REQUIRED IFF STRELKA: Sample ID for for normal sample

Known Issues