75
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchCreated page with '= Software Page Overview = This page points to downloads, documentation, and papers for software that is written here at the [http://genome.sph.umich.edu Center for Statistical …'
= Software Page Overview =
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]
= [[Read Mapping]] =
==[[Karma|Karma]]==
Our fast short read aligner, which generates [[Mapping Quality Scores]]
==[[Karma-colorspace|Karma-ColorSpace]]==
QUICKSTART on mapping color space reads
==[[Examples|Examples]]==
Sample command lines with discussion
==[[MapabilityScores]]==
Definitions of various mappability scores adopted at UCSC genome browser.
= 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 Utilities =
==[[FastQ Validator]]==
Check that a FASTQ file conforms to specification.
==[[BamIdentityCheck]]==
Check that mapped reads are consistent with known genotypes for each individual.
= File Readers =
==[[BamFile]]==
Reads a BAM/SAM file.
==[[FastQFile]]==
Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
= File Conversion =
==[[bam2FastQ]]==
Convert BAM files into FastQ files
= [[Links to Sequence Analysis Tools|Other Useful Links]] =
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]
= [[Read Mapping]] =
==[[Karma|Karma]]==
Our fast short read aligner, which generates [[Mapping Quality Scores]]
==[[Karma-colorspace|Karma-ColorSpace]]==
QUICKSTART on mapping color space reads
==[[Examples|Examples]]==
Sample command lines with discussion
==[[MapabilityScores]]==
Definitions of various mappability scores adopted at UCSC genome browser.
= 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 Utilities =
==[[FastQ Validator]]==
Check that a FASTQ file conforms to specification.
==[[BamIdentityCheck]]==
Check that mapped reads are consistent with known genotypes for each individual.
= File Readers =
==[[BamFile]]==
Reads a BAM/SAM file.
==[[FastQFile]]==
Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
= File Conversion =
==[[bam2FastQ]]==
Convert BAM files into FastQ files
= [[Links to Sequence Analysis Tools|Other Useful Links]] =
