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Variant Discovery in High-Throughput Sequencing Data

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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

RefSeq - gene list format Follow

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    Brian Wiley

    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.

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    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]

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    Brian Wiley

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

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