Difference between revisions of "Software"
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= Quality Control Utilities = | = Quality Control Utilities = | ||
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[[C++ Executable: fastQValidator|FastQValidator]] -- Check that a FASTQ file conforms to specification. | [[C++ Executable: fastQValidator|FastQValidator]] -- Check that a FASTQ file conforms to specification. | ||
| − | [[ | + | [[GenotypeIDcheck]] -- Check that mapped reads are consistent with known genotypes for each individual. |
== File Readers == | == File Readers == | ||
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[[C++ Library: libbam|BamFile]] -- Reads a BAM/SAM file. | [[C++ Library: libbam|BamFile]] -- Reads a BAM/SAM file. | ||
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== File Conversion == | == File Conversion == | ||
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[[bam2FastQ]] -- Convert BAM files into FastQ files | [[bam2FastQ]] -- Convert BAM files into FastQ files | ||
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= [[Links to Sequence Analysis Tools|Other Useful Links]] = | = [[Links to Sequence Analysis Tools|Other Useful Links]] = | ||
Revision as of 11:19, 21 June 2010
Software Page Overview
This page points to downloads, documentation, and papers for software that is written here at the Center for Statistical Genetics
Read Mapping
Karma
Our fast short read aligner, which generates Mapping Quality Scores
Karma-ColorSpace
QUICKSTART on mapping color space reads
Examples
Sample command lines with discussion
MapabilityScores
Definitions of various mappability scores adopted at UCSC genome browser.
Evaluation of Mappers
baseQualityCheck is a mature tool to calculate the observed base quality vs. empirical base quality.
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
Validators
FastQValidator -- Check that a FASTQ file conforms to specification.
GenotypeIDcheck -- 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
