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970 bytes removed, 11:22, 8 April 2010
move most detail to Software page - this tightens up the Main page for easier browsing
== Sequence Analysis Tools ==
We are developing several tools [[Software]] for the analysis of next generation sequence data.
=== [[# Read Mapping]] === [[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]] with [[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 === with [[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 === Annotations using [[vcfCodingSnps]] -- Annotate coding variants in a VCF file. === # Quality Control Utilities === control using [[C++ Executable: fastQValidator|FastQValidator]] -- Check that a FASTQ file conforms to specification. , and [[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual. === # File Readers ===using [[C++ Library: libbam|BamFile]] -- Reads a BAM/SAM file.  and [[C++ Library: libfqf|FastQFile]] -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read. === # File Conversion ===Conversions using [[bam2FastQ]] -- Convert BAM files into FastQ files=== [[Links to Sequence Analysis Tools|Other Useful Links]] ===
== Projects ==

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