Difference between revisions of "Main Page"
| Line 50: | Line 50: | ||
[[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual. | [[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual. | ||
| + | === File Conversion === | ||
| + | [[bam2FastQ]] -- Convert BAM files into FastQ files | ||
=== [[Links to Sequence Analysis Tools|Other Useful Links]] === | === [[Links to Sequence Analysis Tools|Other Useful Links]] === | ||
Revision as of 15:09, 18 March 2010
|
Abecasis Group Wiki
|
Welcome!
Welcome to our brand new wiki!
If you would like to contribute, log-in or create an account. We recommend using your e-mail address or Michigan uniqname as your user id.
For basic instructions, see the Wikipedia Tutorial.
Sequence Analysis Tools
We are developing several tools for the analysis of next generation sequence data.
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
FastQ Validator -- Check that a FASTQ file conforms to specification.
FastQFile -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
BamIdentityCheck -- Check that mapped reads are consistent with known genotypes for each individual.
File Conversion
bam2FastQ -- Convert BAM files into FastQ files
Other Useful Links
Projects
SardiNIA - The SardiNIA longitudinal study of aging.
1000 Genomes Project Pilot 1 SNP Calling
Learn Genetics
Faculty in the group teach in a variety of formal and informal settings. Class notes and relevant discussion are archived here.
Abecasis Group Meeting
2:30-4:00 p.m. on Fridays, room 2610, SPH I. Please note April 9, please use room 2690, SPH I.
