Software

Software

Due to increasing volume of next generation sequencing and genotyping data, we have created these created C++ library and tools that use that library.

This page points to downloads, documentation, and papers for software that is written here at the Center for Statistical Genetics

StatGen C++ Software

We have developed a C++ library and tools for handling and analyzing next generation sequencing and genotyping data.

Library

The library contains easy-to-use APIs for developing tools for processing and analyzing next generation sequencing and genotyping data. Allows easy processing of SAM/BAM, GLF, and FASTQ (VCF is coming).

More information on the library can be found at: C++ Library: libStatGen

The library can be downloaded at: libStatGen Download

Programs/Tools

Follow the program links for more information on obtaining the tool. Some tools are packaged together.

SAM/BAM

General Tools

• QPLOT - Calculate & plot summary statistics
• Validate – Check file format & print statistics
• VerifyBamID – Check sample identities for contamination/sample swap
  • Genotype concordance based detection
  • Estimate based on population allele frequencies without genotype data
• Diff - Print the diffs between 2 bams
• Stats - Generate some statistics for a SAM/BAM file

Rewrite SAM/BAM file

• Convert – Convert between SAM & BAM
• SplitBam – Split into 1 file per Read Group
• SplitChromosome – Split into 1 file per Chromosome
• WriteRegion – Write only reads in the specified region and/or have the specified read name
• Pileup – Pileup every base or just bases in specified region and write VCF
• ReadIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file

Update the File

• SuperDeDuper - Determine duplicate alignments, either marking or removing the lower quality duplicates. In addition, it may modify paired-end reads where the ends overlap by soft clipping the end with the lower quality bases in the region of overlap.
• RGMergeBam – Merge sorted BAM files adding Read Groups
• PolishBam – Add/Update header lines & add RG tag to each record
• TrimBam – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
• Filter – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
• Revert - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
• 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

Helper Tools to Print Readable Information

• DumpHeader - Print the File Header to the screen.
• DumpRefInfo - Print the reference information from the SAM/BAM header.
• DumpIndex - Print the BAM Index to the screen in a readable format
• ReadReference - Print the reference string for the specified region to the screen.

FASTQ

• fastqValidator - validate a FASTQ file
  • Reports errors for badly formatted files
  • Reports Base Composition Statistics (%reads at each read index)

Other Tools

• createUMref - Create the University of Michigan formatted reference used by many of our tools
• thunderVCF
• vcfCooker – Manipulate, filter, summarize VCF/BED file in various forms
• VcfGenomeStat – Print flanking sequences and how often they appear for input VCF file

Requested Tools

BAM to FASTQ

Other Tools

Read Mapping

• Karma - Our fast short read aligner, which generates Mapping Quality Scores
• Karma-ColorSpace - QUICKSTART on mapping color space reads
• baseQualityCheck - a mature tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers)

• Examples - Sample command lines with discussion

• MapabilityScores - Definitions of various mappability scores adopted at UCSC genome browser.

SAM/BAM

• Recalibrator – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - Available upon request
• Deduper – Mark or remove duplicates - Coming Soon

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
• polymutt - Variant and de novo mutation detection in families (nuclear or extended pedigrees) from sequencing

Variant Annotation

• vcfCodingSnps - Annotate coding variants in a VCF file.

Quality Control

• GenotypeIDcheck - Check that mapped reads are consistent with known genotypes for each individual.

File Conversion

• bam2FastQ - Convert BAM files into FastQ files

Other Useful Links

Links to Sequence Analysis Tools

Other

ASHG 2010 Poster: C++ library & tools for next generation sequence data