Software

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>=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

A library and set of set of tools developed for handling and analyzing next generation sequencing and genotyping data.

Download

StatGen Download

Library

  • C++ Library: libStatGen - Library containing easy-to-use APIs for developing tools for processing and analyzing next generation sequencing and genotyping data. Allows easy processing of SAM/BAM, GLF, FASTQ.


Tools

SAM/BAM

General Tools

  • QPLOT - Calculate & plot summary statistics
  • BamValidator – Check file format & print statistics
  • Convert – Convert between SAM & BAM
  • WriteRegion – Write only reads in the specified region
  • Pileup – Pileup every base or just bases in specified region and write VCF - Coming Soon
  • 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

  • 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


Split the File


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

  • vcfCooker – Manipulate, filter, summarize VCF/BED file in various forms - Coming Soon
  • VcfGenomeStat – Print flanking sequences and how often they appear for input VCF file

Other Tools

Read Mapping

  • Examples - Sample command lines with discussion
  • MapabilityScores - Definitions of various mappability scores adopted at UCSC genome browser.


SAM/BAM

  • VerifyBamID – Check sample identities for contamination/sample swap
    • Genotype concordance based detection
    • Estimate based on population allele frequencies without genotype data
  • 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

Variant Annotation

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