What is the most rational way and software for comapring a set of NGS WGS VCF files produced with NextGene software?
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6.5 years ago
vassialk ▴ 200

What is the most rational way and software for comapring a set of NGS WGS VCF files produced with NextGene software? I have found a Genematrix service and Rsubread R package. Is there any other software which can compare VCFs and produce a meaningful clear report showing the differences with high-quality charts, graphs? Thanks.

ngs wgs sequencing • 1.7k views
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6.5 years ago
rbagnall ★ 1.7k

See:

How to compare 2 VCF files

and have a look at Variant Evaluation by GATK, which compares two vcf files and produces a report that shows intersection of variants, number of unique calls, number in dbSNP, etc.

http://gatkforums.broadinstitute.org/discussion/48/using-varianteval

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