Software

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.

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

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