487
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Variant Annotation
=Software=
=Software=
Due to increasing volume of next generation sequencing and genotyping data, we have created these created C++ library and tools that use that library.
Due to increasing volume of next generation sequencing and genotyping data, we have created these C++ library and tools that use that library.
This page points to downloads, documentation, and papers for software that is written here at the [http://genome.sph.umich.edu Center for Statistical Genetics]
This page points to downloads, documentation, and papers for software that is written here at the [http://genome.sph.umich.edu Center for Statistical Genetics]
If you have any questions or comments, please email Mary Kate Trost (mktrost@umich.edu).
If you have any questions or comments, please email Mary Kate Wing (mktrost@umich.edu).
=StatGen C++ Software=
=StatGen C++ Software=
=== SAM/BAM ===
=== SAM/BAM ===
*[[QPLOT]] - Calculate & plot summary statistics
*[[QPLOT]] - Calculate & plot summary statistics
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
**Genotype concordance based detection
**Genotype concordance based detection
**Estimate based on population allele frequencies without genotype data
**Estimate based on population allele frequencies without genotype data
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
==== BAM Util Tools ====
{{BamUtilPrograms}}
=== FASTQ ===
=== FASTQ ===
**Reports Base Composition Statistics (%reads at each read index)
**Reports Base Composition Statistics (%reads at each read index)
=== Meta Analysis ===
* [[Rare-Metal-Worker|RAREMETALWORKER - generate summary level statistics for meta analysis using Rare-Metal]]
* [[Rare-Metal|RAREMETAL - perform genome-wide meta analysis of rare variants]]
=== Other Tools ===
=== Other Tools ===
=== Requested Tools ===
=== Requested Tools ===
=Other Tools=
=Other Tools=
* [[samtools-hybrid]] - Since many of our tools still rely on GLF files and samtools stopped supporting GLF files, we created a version of samtools that still supports pileup to GLF files AND incorporates the updated BAQ logic. This version is called samtools-hybrid That code can be downloaded at: https://github.com/statgen/samtools-0.1.7a-hybrid
*[[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]]
*[[baseQualityCheck]] - tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers)
*[[baseQualityCheck]] - a mature tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers)
== Variant Calling ==
== Variant Calling ==
* [[glfSingle]] - Variant calling for a single, deeply sequenced individual
* [[glfSingle]] - Variant calling for a single, deeply sequenced individual
* [[glfMultiples]] - Variant calling for multiple, unrelated individuals
* [[glfMultiples]] - Variant calling for multiple, unrelated individuals
* [[Polymutt:_a_tool_for_calling_polymorphism_and_de_novo_mutations|polymutt]] - Variant and ''de novo'' mutation detection in families (nuclear or extended pedigrees) from sequencing
* [[Polymutt|polymutt]] - Variant and ''de novo'' mutation detection in families (nuclear or extended pedigrees) from sequencing
== Variant Annotation ==
== Variant Annotation ==
*[[vcfCodingSnps]] - Annotate coding variants in a VCF file.
*[[vcfCodingSnps]] - Annotate coding variants in a VCF file.
== Quality Control ==
== Genotype Imputation ==
*[[GenotypeIDcheck]] - Check that mapped reads are consistent with known genotypes for each individual.
*[[Minimac3]] - Fast and Efficient Genotype Imputation.
== Additional Pedigree & Sequence Analysis Tools ==
Can be found at: http://sph.umich.edu/csg/abecasis/software.html
= Other Useful Links =
= Other Useful Links =
