Mapper
|
BWA
|
No canonical (many)
|
BWA
|
BWA
|
BWA/Bowtie
|
Variant caller
|
Atlas2
|
No canonical (many)
|
GATK
|
Samtools mpileup
|
Samtools/GATK, Varscan
|
Annotation
|
Cassandra
|
snpEff, AlleleFrequency
|
snpEff, ANNOVAR
|
Bioconductor
|
ANNOVAR
|
Visualization
|
Built-in browser
|
Built-in browser
|
Links to IGV
|
Built-in browser
|
No
|
Runs on local hardware
|
No*
|
Yes
|
No
|
Yes
|
Yes
|
Runs on cloud infrastructure
|
Yes
|
Yes
|
Yes
|
Jobs queued to public server
|
No
|
HIPAA compliant
|
Yes
|
No
|
No
|
No
|
Not Applicable (local only)
|
Requires setup configuration
|
No
|
Yes
|
No
|
Yes
|
Yes
|
Can add tools independently
|
Yes
|
Yes
|
By request
|
No
|
No
|
Data sharing & collaboration
|
Yes
|
Yes
|
No
|
No
|
No
|