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PVCTools


  PVCTools is Parallel Variation Calling Tools, which tries to call variation using multiple threads. Basically, the reference genome will be split into small pieces, and corresponding alignment BAM files will be extracted. Under this way, it will speed up the process of variation calling a lot.

  PVCTools majorly contains 8 modules: all, SplitFA, SegmentFA, SplitBAM, SegmentBAM, Submit, SwitchVCF and SmallFA.


PVCTools User Manual

  User Manual download: Download

  Prerequisites

  Install

  To install PVCTools, please follow:

  •    # unzip PVCTools_alpha_v*.zip
  •    # make

PVCTools download

  •   Lastet version: PVCTools V3.3
  •   Update: support GATK and freebayes!
  •   Past version: PVCTools V3.2
  •   update: fix the wrong position for last piece of each chromosome!

Results of test data

Single Sample
samtools GATK freebayes sambamba PCVTools
arabidopsis VCF
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VCF
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VCF
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VCF
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VCF
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rice VCF
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VCF
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VCF
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VCF
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VCF
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human VCF
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VCF
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VCF
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VCF
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VCF
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tobacco VCF
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VCF
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VCF
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VCF
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VCF
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Multiple Sample
samtools GATK freebayes sambamba PCVTools
arabidopsis VCF
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VCF
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VCF
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VCF
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VCF
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rice VCF
Download data
VCF
Download data
VCF
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VCF
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VCF
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human VCF
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VCF
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VCF
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VCF
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VCF
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tobacco VCF
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VCF
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VCF
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VCF
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VCF
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Citation

  •   1. Li Z,Lu P,Zhang J,Zhang H,Xu Y,Jin J#:System comparisonof population genetic variation calling tools. Tobacco Science and Technology, 2017
  •   2. Jin J,Liu L,Li Z,Lu P,Xu Y,Cao P# Hu D#: PVCTools: Parallel Variation Calling Tools.2017. In prepared