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

Pileup Follow

1 comment

  • Avatar
    Jose Camacho Valenzuela


    I am running Pileup with GATK I would like to obtain an output file containing also the read depth of both the REF and ALT alleles on my input bam (I am indicating 2 input bams, one for normal and the other for tumor).

    An example of my desired output is this:

    How could I obtain these extra columns of read depth of REF and ALT of my input bams?

    I will STRONGLY APPRECIATE your help on this matter. Thank you SO MUCH IN ADVANCE!


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk