What input files does the GATK accept require

IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here

created by GATK_Team

on 2017-12-26

Analyses done with the GATK typically involve several (though not necessarily all) of the following inputs:

- Reference genome sequence in [FASTA format](https://software.broadinstitute.org/gatk/documentation/article?id=11013)

- Unmapped sequencing data in [uBAM format](https://software.broadinstitute.org/gatk/documentation/article?id=11008) (alternative to FASTQ)

- Mapped sequencing data in [SAM, BAM or CRAM format](https://software.broadinstitute.org/gatk/documentation/article?id=11014)

- List of [intervals](https://software.broadinstitute.org/gatk/documentation/article?id=11009)

- Variant calls in [VCF format](https://software.broadinstitute.org/gatk/documentation/article?id=11005) or [GVCF format](https://software.broadinstitute.org/gatk/documentation/article?id=11004) (can be gzipped)

- Supplementary resources (e.g. known variants) as documented by the relevant tools