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= Software Page Overview =
=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.


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]


=StatGen C++ Software=
A library and set of set of tools developed for handling and analyzing next generation sequencing and genotyping data.


= [[Read Mapping]] =
== Download ==


==[[Karma|Karma]]==
Our fast short read aligner, which generates [[Mapping Quality Scores]]


==[[Karma-colorspace|Karma-ColorSpace]]==
== Library ==
QUICKSTART on mapping color space reads
* [[C++ Library: libStatGen]] - Library containing easy-to-use APIs for developing tools for processing and analyzing next generation sequencing and genotyping data.  Allows easy processing of SAM/BAM, GLF, FASTQ.


==[[Examples|Examples]]==
Sample command lines with discussion


==[[MapabilityScores]]==
== Tools ==
Definitions of various mappability scores adopted at UCSC genome browser.
=== SAM/BAM ===


==Evaluation of Mappers==
==== General Tools ====
[[baseQualityCheck]] is a mature tool to calculate the observed base quality vs. empirical base quality.
*[[QPLOT]] - Calculate & plot summary statistics
*[[BamValidator]] – Check file format & print statistics
*[[C++ Executable: bam#convert|Convert]] – Convert between SAM & BAM
*[[C++ Executable: bam#writeRegion|WriteRegion]] – Write only reads in the specified region
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF - <span style="color:#D2691E">Coming Soon</span>
*[[C++ Executable: bam#readIndexedBam|ReadIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file


= Variant Calling =


==[[glfSingle]]==
==== Update the File ====
Variant calling for a single, deeply sequenced individual
*[[RGMergeBam]] – Merge sorted BAM files adding Read Groups
*[[PolishBam]] – Add/Update header lines & add RG tag to each record
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[C++ Executable: bam#filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high


==[[glfTrio]]==
Variant calling for a single, deeply sequenced nuclear family with two parents and one child


==[[glfMultiples]]==
==== Split the File ====
Variant calling for multiple, unrelated individuals
*[[SplitBam]] – Split into 1 file per Read Group
*[[C++ Executable: bam#splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome


= Variant Annotation =


==[[vcfCodingSnps]]==
==== Helper Tools to Print Readable Information ====
Annotate coding variants in a VCF file.
*[[C++ Executable: bam#dumpHeader|DumpHeader]] - Print the File Header to the screen.
*[[C++ Executable: bam#dumpRefInfo|DumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[C++ Executable: bam#dumpIndex|DumpIndex]] - Print the BAM Index to the screen in a readable format
*[[C++ Executable: bam#readReference|ReadReference]] - Print the reference string for the specified region to the screen.


= Quality Control Utilities =


== Validators ==


[[C++ Executable: fastQValidator|FastQValidator]] -- Check that a FASTQ file conforms to specification.
=== FASTQ ===
* [[FastQValidator|fastqValidator]] - validate a FASTQ file
**Reports errors for badly formatted files
**Reports Base Composition Statistics (%reads at each read index)


[[GenotypeIDcheck]] -- Check that mapped reads are consistent with known genotypes for each individual.


[[BamValidator]] -- Checks that a SAM/BAM file conforms to specification and generates some statistics on the file.
=== Other Tools ===
*[[VcfGenomeStat]] – Print flanking sequences and how often they appear for input VCF file


== File Readers ==
=Other Tools=


[[C++ Library: libbam|BamFile]] -- Reads a BAM/SAM file.
== [[Read Mapping]] ==
*[[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]]
*[[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads
*[[baseQualityCheck]] - a mature tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers)


[[C++ Library: libfqf|FastQFile]] -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
*[[Examples|Examples]] - Sample command lines with discussion
 
*[[MapabilityScores]] - Definitions of various mappability scores adopted at UCSC genome browser.
 
 
 
==SAM/BAM==
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
**Genotype concordance based detection
**Estimate based on population allele frequencies without genotype data
*Recalibrator – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - <span style="color:#D2691E">Available upon request</span>
*Deduper – Mark or remove duplicates - <span style="color:#D2691E">Coming Soon</span>
 
== Variant Calling ==
* [[glfSingle]] - Variant calling for a single, deeply sequenced individual
* [[glfTrio]]- Variant calling for a single, deeply sequenced nuclear family with two parents and one child
* [[glfMultiples]] - Variant calling for multiple, unrelated individuals
 
== Variant Annotation ==
*[[vcfCodingSnps]] - Annotate coding variants in a VCF file.
 
== Quality Control ==
*[[GenotypeIDcheck]] - Check that mapped reads are consistent with known genotypes for each individual.


== File Conversion ==
== File Conversion ==
 
*[[bam2FastQ]] - Convert BAM files into FastQ files
[[bam2FastQ]] -- Convert BAM files into FastQ files




= [[Links to Sequence Analysis Tools|Other Useful Links]] =
= [[Links to Sequence Analysis Tools|Other Useful Links]] =

Revision as of 01:11, 2 November 2010

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.

This page points to downloads, documentation, and papers for software that is written here at the Center for Statistical Genetics

StatGen C++ Software

A library and set of set of tools developed for handling and analyzing next generation sequencing and genotyping data.

Download

Library

  • C++ Library: libStatGen - Library containing easy-to-use APIs for developing tools for processing and analyzing next generation sequencing and genotyping data. Allows easy processing of SAM/BAM, GLF, FASTQ.


Tools

SAM/BAM

General Tools

  • QPLOT - Calculate & plot summary statistics
  • BamValidator – Check file format & print statistics
  • Convert – Convert between SAM & BAM
  • WriteRegion – Write only reads in the specified region
  • Pileup – Pileup every base or just bases in specified region and write VCF - Coming Soon
  • ReadIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file


Update the File

  • RGMergeBam – Merge sorted BAM files adding Read Groups
  • PolishBam – Add/Update header lines & add RG tag to each record
  • TrimBam – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
  • Filter – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high


Split the File


Helper Tools to Print Readable Information

  • DumpHeader - Print the File Header to the screen.
  • DumpRefInfo - Print the reference information from the SAM/BAM header.
  • DumpIndex - Print the BAM Index to the screen in a readable format
  • ReadReference - Print the reference string for the specified region to the screen.


FASTQ

  • fastqValidator - validate a FASTQ file
    • Reports errors for badly formatted files
    • Reports Base Composition Statistics (%reads at each read index)


Other Tools

  • VcfGenomeStat – Print flanking sequences and how often they appear for input VCF file

Other Tools

Read Mapping

  • Examples - Sample command lines with discussion
  • MapabilityScores - Definitions of various mappability scores adopted at UCSC genome browser.


SAM/BAM

  • VerifyBamID – Check sample identities for contamination/sample swap
    • Genotype concordance based detection
    • Estimate based on population allele frequencies without genotype data
  • Recalibrator – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - Available upon request
  • Deduper – Mark or remove duplicates - Coming Soon

Variant Calling

  • glfSingle - Variant calling for a single, deeply sequenced individual
  • glfTrio- Variant calling for a single, deeply sequenced nuclear family with two parents and one child
  • glfMultiples - Variant calling for multiple, unrelated individuals

Variant Annotation

Quality Control

  • GenotypeIDcheck - Check that mapped reads are consistent with known genotypes for each individual.

File Conversion

  • bam2FastQ - Convert BAM files into FastQ files


Other Useful Links

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