- 1 Software Page Overview
- 2 Read Mapping
- 3 Variant Calling
- 4 Variant Annotation
- 5 Quality Control Utilities
- 6 File Readers
- 7 File Conversion
- 8 Other Useful Links
Software Page Overview
This page points to downloads, documentation, and papers for software that is written here at the Center for Statistical Genetics
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.
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
Annotate coding variants in a VCF file.
Quality Control Utilities
Check that a FASTQ file conforms to specification.
Check that mapped reads are consistent with known genotypes for each individual.
Reads a BAM/SAM file.
Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
Convert BAM files into FastQ files