Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

HaplotypeCaller Follow

1 comment

  • Avatar

    Hi GATK Team, 

    I noticed the message "Input bam file(s) from which to make variant calls" in the Input subsection. Further down, I noticed in the Haplotype Specific Arguments section that the --input argument can take CRAM/SAM/BAM files as input. I was wondering if the program has a preference for input file type? By that I mean, "under the hood" does the program have to do some kind of conversion between file types if one input is offered versus another? Is it computationally more efficient to give the program one type over the others?

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk