gatk-tools-javaTools 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.
htsjdkjava framework used by picard and GATK to access reads in bam files and variants in VCF files
picardJava tool set using htsjdk to perform tasks on fastq, sam, bam and vcf files. Loop-based code, son no (easy) multiprocessor support.
GATK-frameworkJava-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.
GATK-toolsA set of tools using the GATK-framework for analysis of bam and vcf files.
htslibC-framework for manipulation of BAM, CRAM, and VCF files.
samtoolsTool set built using htslib for manipulation of sam files.
gamgeeC-framework further extending htslib.
- Google maps
- genome browser