Are there any new/novel R packages and other software to compare a 100 of VCF files?

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8.1 years ago

genomicswolf ▴ 20

Are there any new/novel R packages and other software to compare a 100 of VCF files? Tried GATK and VCF tools and nextGene. Need a better solution for a hunderds of VCFs.

vcf r • 1.5k views

ADD COMMENT • link 8.1 years ago by genomicswolf ▴ 20

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Could you be more specific on what you aim to achieve? "Compare" is quite generic.

ADD REPLY • link 8.1 years ago by WouterDeCoster 47k

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find differences in vcfs, thx

ADD REPLY • link 8.1 years ago by genomicswolf ▴ 20

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Oh right now I understand. Differences.

Could you be more specific on what you aim to achieve? "Differences" is quite generic.

ADD REPLY • link 8.1 years ago by WouterDeCoster 47k

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Not new and not sure whether it fits your needs but did you take a look at the VariantAnnotation bioconductor package?

ADD REPLY • link 8.1 years ago by ddiez ★ 2.0k

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