Somalier v0.2.6 – fast Sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs

somalier v0.2.6

:: DESCRIPTION

somalier extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

somalier

:: MORE INFORMATION

Citation:

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches
Brent S Pedersen, Preeti J Bhetariya, Joe Brown, Gabor Marth, Randy L Jensen, Mary P Bronner, Hunter R Underhill, Aaron R. Quinlan.

Vcfanno v0.3.2 – Annotate a VCF with other VCFs/BEDs/tabixed files

Vcfanno v0.3.2

:: DESCRIPTION

Vcfanno annotates a VCF with any number of sorted and tabixed input BED, BAM, and VCF files in parallel. It does this by finding overlaps as it streams over the data and applying user-defined operations on the overlapping annotations.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GO

:: DOWNLOAD

Vcfanno

:: MORE INFORMATION

Citation:

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.
Vcfanno: fast, flexible annotation of genetic variants.
Pedersen BS, Layer RM, Quinlan AR.

VCFtools 0.1.13 – Program Package designed for working with VCF files

VCFtools 0.1.13

:: DESCRIPTION

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project.The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.

::DEVELOPER

VCFtools Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • perl
  • C++ Compiler

:: DOWNLOAD

 VCFtools

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

testvariants2VCF v2 – Testvariants to VCF

testvariants2VCF v2

:: DESCRIPTION

The perl script testvariants2VCF-v2.pl converts the output of the cgatools “testvariants” command into a multi-sample VCF file. The script requires a cgatools installation and access to a reference genome encoded in .crr format

::DEVELOPER

Complete Genomics, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 testvariants2VCF

:: MORE INFORMATION