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

Articles in this section

See more

RefSeq - gene list format Follow

Avatar
GATK Team
  • Updated

From the NCBI RefSeq website

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq is a foundation for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.

Several GATK tools accept a RefSeq-formatted gene list. Mind you, there are many file format flavors of ReqSeq; we've chosen to use the table dump format produced by the UCSC genome table browser.

Generating RefSeq files

Go to the UCSC genome table browser. There are many output options; here are the settings we care about: 

assembly: [be sure to pick the same [reference genome build](https://software.broadinstitute.org/gatk/documentation/article.php?id=11011) that you're working with]
group:    Genes and Gene Prediction Tracks
track:    RefSeq Genes
table:    refGene

Choose a good output filename, something like my_organism.geneTrack.refSeq, and click the get output button. You now have your initial RefSeq file, which may not be sorted, and may contain non-standard contigs. You may need to re-sort the file and remove any contigs to match exactly the sequence dictionary of the reference build you're working with.

Warning

The GATK automatically adjusts the start and stop position of the records from zero-based half-open intervals (UCSC standard) to one-based closed intervals.

For example:

The first 19 bases in Chromosome one:
Chr1:0-19 (UCSC system)
Chr1:1-19 (GATK)

All of the GATK output is also in this format, so if you're using other tools or scripts to process RefSeq or GATK output files, you should be aware of this difference.

Related articles

3 comments

Sort by Date Votes
  • Avatar
    Brian Wiley

    Might want to specify the output file format...BED, Gtf, All fields?

    0
    Comment actions Permalink
  • Avatar
    Brian Wiley
    • Edited

    Ah hah!!! Like this https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-methods-and-algorithms/Performing_sequence_coverage_analysis.md

    You need to select "all fields" from UCSC table browser and remove header row.

    0
    Comment actions Permalink
  • Avatar
    Lijia Yu

    Does anyone know that how to sort the Refseq file to match exactly the sequence dictionary of the reference build?

    ##### ERROR MESSAGE: Input files /home/Ly/refGene.sorted.txt and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information. Error details: The contig order in /home/Ly/refGene.sorted.txt and reference is not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files..
    ##### ERROR /home/Ly/refGene.sorted.txt contigs = [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr17_ctg5_hap1, chr17_gl000205_random, chr18, chr19, chr19_gl000209_random, chr1_gl000191_random, chr1_gl000192_random, chr2, chr20, chr21, chr22, chr3, chr4, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7, chr7_gl000195_random, chr8, chr9, chrM, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000215, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000227, chrUn_gl000228, chrUn_gl000241, chrX, chrY]
    ##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk