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| | This page points to downloads, documentation, and papers for software that is written here at the [http://genome.sph.umich.edu Center for Statistical Genetics] | | This page points to downloads, documentation, and papers for software that is written here at the [http://genome.sph.umich.edu Center for Statistical Genetics] |
| | | | |
| − | If you have any questions or comments, please email Mary Kate Trost (mktrost@umich.edu). | + | If you have any questions or comments, please email Mary Kate Wing (mktrost@umich.edu). |
| | | | |
| | =StatGen C++ Software= | | =StatGen C++ Software= |
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| | ==== BAM Util Tools ==== | | ==== BAM Util Tools ==== |
| − | The following tools are part of the [[BamUtil|BamUtil program]].
| + | {{BamUtilPrograms}} |
| − | | |
| − | '''QC/Stats'''
| |
| − | *[[BamUtil: validate|validate]] – Check file format & print statistics
| |
| − | *[[BamUtil: diff|diff]] - Print the diffs between 2 bams
| |
| − | *[[BamUtil: stats|stats]] - Generate some statistics for a SAM/BAM file
| |
| − | '''Rewrite SAM/BAM file'''
| |
| − | *[[BamUtil: convert|convert]] – Convert between SAM & BAM
| |
| − | *[[BamUtil: splitBam|splitBam]] – Split into 1 file per Read Group
| |
| − | *[[BamUtil: splitChromosome|splitChromosome]] – Split into 1 file per Chromosome
| |
| − | *[[BamUtil: writeRegion|writeRegion]] – Write only reads in the specified region and/or have the specified read name
| |
| − | *[[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
| |
| − | *[[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
| |
| − | '''File Updates'''
| |
| − | *[[BamUtil: dedup|dedup]] – Mark or remove duplicates, can also perform recalibration - <span style="color:#D2691E">Coming Soon</span>
| |
| − | *[[BamUtil: recab|recab]] - Recalibrate – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - <span style="color:#D2691E">Coming Soon</span>
| |
| − | *[[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap
| |
| − | *[[BamUtil: filter|filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
| |
| − | *[[BamUtil: revert|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
| |
| − | *[[BamUtil: squeeze|squeeze]] - Reduce files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers
| |
| − | *[[BamUtil: trimBam| trimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
| |
| − | *[[BamUtil: polishBam|polishBam]] – Add/Update header lines & add RG tag to each record
| |
| − | *[[BamUtil: rgMergeBam|rgMergeBam]] – Merge sorted BAM files adding Read Groups
| |
| − | | |
| − | '''Additional Tools'''
| |
| − | * [[BamUtil: bam2FastQ|bam2FastQ]] - Convert the specified BAM file to fastQs
| |
| − | | |
| − | '''Helper Tools to Print Readable Information'''
| |
| − | *[[BamUtil: dumpHeader|dumpHeader]] - Print the File Header to the screen.
| |
| − | *[[BamUtil: dumpRefInfo|dumpRefInfo]] - Print the reference information from the SAM/BAM header.
| |
| − | *[[BamUtil: dumpIndex|dumpIndex]] - Print the BAM Index to the screen in a readable format
| |
| − | *[[BamUtil: dumpAsp|dumpAsp]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
| |
| − | *[[BamUtil: readReference|readReference]] - Print the reference string for the specified region to the screen.
| |
| − | | |
| | | | |
| | === FASTQ === | | === FASTQ === |
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| | **Reports Base Composition Statistics (%reads at each read index) | | **Reports Base Composition Statistics (%reads at each read index) |
| | | | |
| | + | |
| | + | === Meta Analysis === |
| | + | * [[Rare-Metal-Worker|RAREMETALWORKER - generate summary level statistics for meta analysis using Rare-Metal]] |
| | + | * [[Rare-Metal|RAREMETAL - perform genome-wide meta analysis of rare variants]] |
| | | | |
| | === Other Tools === | | === Other Tools === |
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| | | | |
| | === Requested Tools === | | === Requested Tools === |
| − | [[BAM to FASTQ]]
| |
| | | | |
| | =Other Tools= | | =Other Tools= |
| | | | |
| − | * samtools-hybrid - Since many of our tools still rely on GLF files and samtools stopped supporting GLF files, we created a version of samtools that still supports pileup to GLF files AND incorporates the updated BAQ logic. This version is called samtools-hybrid That code can be downloaded at: https://github.com/statgen/samtools-0.1.7a-hybrid | + | * [[samtools-hybrid]] - Since many of our tools still rely on GLF files and samtools stopped supporting GLF files, we created a version of samtools that still supports pileup to GLF files AND incorporates the updated BAQ logic. This version is called samtools-hybrid That code can be downloaded at: https://github.com/statgen/samtools-0.1.7a-hybrid |
| | *[[baseQualityCheck]] - tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers) | | *[[baseQualityCheck]] - tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers) |
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| | == Variant Annotation == | | == Variant Annotation == |
| | *[[vcfCodingSnps]] - Annotate coding variants in a VCF file. | | *[[vcfCodingSnps]] - Annotate coding variants in a VCF file. |
| | + | |
| | + | == Genotype Imputation == |
| | + | *[[Minimac3]] - Fast and Efficient Genotype Imputation. |
| | | | |
| | == Additional Pedigree & Sequence Analysis Tools == | | == Additional Pedigree & Sequence Analysis Tools == |
