A big data toolset for family-based sequencing data analysis

• Dependencies
• Availability
• Installing VM bundling with SeqHBase
• Installing pre-compiled release
• Modifying parameters in configuration file

• Variant
• Variation
• Coverage (Read Depth)

• De novo and autosomal recessive (or X-linked) screens
• Compound heterozygous screens

SeqHBase provides a number of features and functionalities. It extracts variant, variation, and coverage (read-depth) information from three commonly used file formats, including tab (or comma) delimited variant annotation files (e.g. CSV files), VCF files, and compressed BAM files.

SeqHBase is developed by Dr. Max M. He et al..  This toolset is free to academic community.  Please feel free to contact Max with any questions, feedback, or bug reports at maxy dot he at gmail dot com

We are interested to hear your comments and feedback as features and improvements will be added in future releases. If you have ideas for improving SeqHBase or features you wish to add, we will be glad to hear about them.

As SeqHBase builds on top of Apache Hadoop and HBase, which itself relies on Hadoop and HBase for job execution, the installation requires a working Hadoop and HBase setup, such as Amazon's Elastic MapReduce service of Amazon Web Services (AWS) or an in-house Hadoop and HBase cluster. For more information about setting up an Apache Hadoop and HBase cluster, please refer to http://hadoop.apache.org/ and http://hbase.apache.org/.

• Dependencies: We developed and tested SeqHBase with the following dependencies:
• Hadoop version 2.6.0 + HBase version 0.98.11 -> SeqHBase1.10 (latest version)
• Hadoop version 1.2.1 + HBase version 0.94.19 -> SeqHBase1.00
• Availability: SeqHBase is a command-line based toolset and is distributed in executable format. SeqHBase-1.10 is the latest version. Users can choose to download either virtual machine (VM) bundling with SeqHBase package (vmSeqHBase1.10 / vmSeqHBase1.00) or pre-compiled release (SeqHBase1.10 / SeqHBase1.00) for local/AWS use. Source code of SeqHBase can be downloaded after obtaining a license agreement with Marshfield Clinic Applied Sciences.
• Installing VM bundling with SeqHBase package
• Download VM bundling with SeqHBase package at here
• Install Oracle VM VirtualBox or similar VirtualBox
• Create a VM by importing the downloaded ova file
• Installing pre-compiled release
• Download the latest SeqHBase release (seqhbase_1.10.tar.gz) at here
• Untar the release into an installation directory of your choice; e.g.,
$ tar zxvf seqhbase_1.10.tar.gz
• Set Hadoop-related variables (e.g., HADOOP_HOME) for your installation
• Set HBASE_HOME to point to your HBase installation
• Modifying parameters in configuration file (server_conf.xml) under folder "conf" of SeqHBase as follows:
• hadoop.home: location of your Hadoop installed
• hadoop.namenode: domain name of your name node
• hadoop.cluster: the value can be either "multiple nodes" if your Hadoop cluster has multiple nodes or "single node" if your Hadoop cluster is single node
• hbase.zookeeper.property.clientPort: property from ZooKeeper's config zoo.cfg. The port at which the clients will connect
• hbase.zookeeper.quorum: comma separated list of servers in the ZooKeeper Quorum. For example, "host1.mydomain.com,host2.mydomain.com". Note: no space following comma
• annotation.columns: the value can be "ProjectID" and the headers of annotated information of the variants

SeqHBase extracts, transforms, and loads (ETL) your variant, variation and quality information from three types of files efficiently.

• Variant:

  annotated variant files generated by ANNOVAR are used to extract variant information, including chromosome number, start position, end position, reference allele, alternative allele, frequency in the 1000 Genome Project and/or the 6500 EPS project, ClinVar, CADD score, biological function, and multiple diverse function relevant scores, such as PolyPhen-2 score, SIFT score, and others. . When developing SeqHBase, we applied ANNOVAR to annotate variants in those sequencing data sets. However, other annotation programs, such as snpEff (http://snpeff.sourceforge.net/), can also be applied in SeqHBase by specifying "annotation.columns" with the annotation header line in your annotation files.

  Command line (Note that the starting "$" symbol indicates the system prompt, do not type in it in your SeqHBase command line):
  $ seqhbase.sh --memory 1024 --csv-file $ANNOTATED_FILE.csv --sample-id $FAM_ID:$IND_ID

  where $FAM_ID is family ID while $IND_ID is individual ID.

  [More Input Parameters]

• Variation:

  VCF files are used to extract variation information, including sample family ID, individual ID, called variant genotypes, coverage (read-depth), and Phred quality scores.

  Type a command in a terminal as follows:
  $ seqhbase.sh --memory 1024 --vcf-file $VCF_FILE.vcf --sample-id $FAM_ID:$IND_ID

  [More Input Parameters]

• Coverage: BAM files are used to extract data regarding coverage of each site of every sequencing sample (~3 billion sites in a WGS). In downstream analyses, the read-depth information can identify if no-call sites are reference-consistent with high quality or reference-inconsistent caused by low quality. A specific function is developed for quickly generating the read depths of each site from BAM files, similar to SAMTools (http://samtools.sourceforge.net/) pileup function. SeqHBase also supports loading coverage information into HBase from a pileup file generated by SAMTools.

  Type a command in a terminal as follows:
  $ seqhbase.sh --memory 4096 --pileup-file $BAM_FILE.bam --sample-id $FAM_ID:$IND_ID

  or

  $ seqhbase.sh --memory 1024 --pileup-file $PILEUP_FILE.gz --sample-id $FAM_ID:IND_ID

  [More Input Parameters]

• De novo and autosomal recessive (or X-linked) screens - command line as follows:
  $ seqhbase.sh --memory 1024 --ped-file $PEDFILE.ped --list-denovo --min-coverage-screen 20 --maf 0.01 --func-list $FUNCLIST --exonic-func-list $EXONICFUNCLIST --query --out $OUTPUT

  [More Input Parameters]

• Compound heterozygous screens - command line as follows:
  $ seqhbase.sh --memory 1024 --ped-file $PEDFILE.ped --list-comp-het --min-coverage-screen 20 --maf 0.01 --func-list $FUNCLIST --exonic-func-list $EXONICFUNCLIST --query --out $OUTPUT

  where $FUNCLIST can be "exonic and/or splicing" and $EXONICFUNCLIST can be started with "nonsynonymous,stopgain,stoploss".

  [More Input Parameters]

• --hadoop-host: specify domain name of Hadoop name node
• --hadoop-home: specify location of your Hadoop installed
• --project: specify a project name
• --polyphen-no-B: phred-based PolyPhen2 score is not annotated to be "B" (benign)
• --sift-no-T: phred-based sift score is not annotated to be "T" (tolerant)
• --ped-file: specify a pedigree file of a family
• --query: analyse a data set with specified pedigree information
• --list-denovo: list de novo and autosomal recessive (or X-linked) mutations in nuclear families
• --list--comp-het: list compound heterozygous mutations in nuclear familiesi
• --min-coverage-screen {20}: specify a minimum coverage (read depth) for screens; the default value is 20
• --maf {0.01}: specify a maximum variant allele frequency in 1000 Genome Project and Exome Project Server; the default value is 0.01
• --func-list: By default, it is "exonic,splicing"
• --exonicFunc-list: By default, it is started with any of the "nonsynonymous,stopgain,stoploss,frameshift"
• --sample-id: specify a sample id by a combination of $FAM_ID + ":" + $IND_ID, where $FAM_ID is family ID while $IND_ID is individual ID

He et al., SeqHBase: a big data toolset for family-based sequencing data analysis. Journal of Medical Genetics, 2015, 52, 282-288. [View PubMed]