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유전체데이터를 다루는 툴이나 스크립트를 만들고자 한다면, 다음의 프로그램, 라이브러리를 눈여겨 보고 응용할 것. 재미있는것은 이제 클라우드상의 데이터도 htsjdk 라이브러리에서 직접 핸들링이 가능해진다는 것이다.

gatk-tools-java

Tools for using picard and gatk with genomics API. getting reads from GA4GH genomics api and exposing them as SAMRecord "Iterable" resource. These will be used for subsequent work on enabling HTSJDK to use API data as input.
GA4GHPicardRunner wrapper around picard tools that allows for INPUTS inot Picard tools to be ga4gh:// usls.
https://github.com/googlegenomics/gatk-tools-java

htsjdk

java framework used by picard and GATK to access reads in bam files and variants in VCF files
https://github.com/samtools/htsjdk

picard

Java tool set using htsjdk to perform tasks on fastq, sam, bam and vcf files. Loop-based code, son no (easy) multiprocessor support.
https://github.com/broadinstitute/picard

GATK-framework

Java-framework future extending htsjdk with capabilities such as accessing pipleups. Defines a set of walkers for developers to extend to traverse bam or vcf files.
https://github.com/broadgsa/gatk

GATK-tools

A set of tools using the GATK-framework for analysis of bam and vcf files.
https://github.com/broadgsa/gatk-protected

htslib

C-framework for manipulation of BAM, CRAM, and VCF files.
https://github.com/broadinstitute/htslib

samtools

Tool set built using htslib for manipulation of sam files.
https://github.com/samtools/samtools.git

gamgee

C-framework further extending htslib. 
https://github.com/broadinstitute/gamgee


Source from: 
http://gatkforums.broadinstitute.org/discussion/4510/writing-custom-tools-htsjdk-vs-picard-vs-gatk