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Revision as of 22:31, 11 May 2010 by Zhanxw (talk | contribs) (Read Mapping)
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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


Our fast short read aligner, which generates Mapping Quality Scores


QUICKSTART on mapping color space reads


Sample command lines with discussion


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


Variant calling for a single, deeply sequenced individual


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


Variant calling for multiple, unrelated individuals

Variant Annotation


Annotate coding variants in a VCF file.

Quality Control Utilities

FastQValidator -- 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

Other Useful Links