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NBISweden / wgs-structvar

Whole Genome Sequenceing Structural Variation Pipelines
GNU General Public License v3.0
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Is vt needed for snpEFF? #43

Closed viklund closed 8 years ago

viklund commented 8 years ago

The snpEff input file is currently preprocessed through vt in the following way:

    sed 's/ID=AD,Number=./ID=AD,Number=R/' "\$vcf" \
        | vt decompose -s - \
        | vt normalize -r $params.ref_fasta - \
        | java -Xmx7G -jar "\$SNPEFFJAR" -formatEff -classic GRCh37.75 \
        > "\$vcf.snpeff"

If vt is not strictly needed we can run snpEff directly on the .bed files. vt is not used for VEP.

pallolason commented 8 years ago

I doubt that effect change will be huge with normalization - its usually just a single base that the coords shift, but preferrably run vt in both cases, VEP and snpeff