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== Sequence Analysis Tools ==
== Sequence Analysis Tools ==
We are developing several tools for the analysis of next generation sequence data.
We are developing [[Software]] for the analysis of next generation sequence data.
# Read Mapping with [[Karma]]
# Variant Calling with [[glfSingle]], [[glfTrio]] and [[glfMultiples]]
# Variant Annotations using [[vcfCodingSnps]]
# Quality control using [[FastQValidator]], and [[BamIdentityCheck]]
[[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads
# File Readers using [[C++ Library: libbam|BamFile]] and [[C++ Library: libfqf|FastQFile]]
# File Conversions using [[bam2FastQ]]
[[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
[[vcfCodingSnps]] -- Annotate coding variants in a VCF file.
[[C++ Executable: fastQValidator|FastQValidator]] -- Check that a FASTQ file conforms to specification.
[[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual.
[[C++ Library: libbam|BamFile]] -- Reads a BAM/SAM file.
[[C++ Library: libfqf|FastQFile]] -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
[[bam2FastQ]] -- Convert BAM files into FastQ files
== Projects ==
== Projects ==
