Reference genome to create intervals list

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Priyadarshini Thirunavukkarasu

• November 08, 2021 13:28

Hello

I have short read exome data. For creating intervals, I converted the reference fasta  file to reference bed file and used this bed file as list of intervals. I used this intervals list for storing all the GVCF files in the database (https://gatk.broadinstitute.org/hc/en-us/articles/360036883491-GenomicsDBImport). Will using the interval list from reference genome lead to error in subsequent steps?. Please advice

 

Priya

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  Pamela Bretscher

  • November 08, 2021 13:59

  Hi Priyadarshini Thirunavukkarasu,

  It is important that the interval list that you use for exome data corresponds to the same exome capture targets. The Broad's exome intervals lists are specific to the custom exome targeting kits used at the Broad, so they may not be suitable depending on the prep kit used for your data. I would recommend getting the appropriate intervals list from the specific sequencing provider that your data is from. 

  Kind regards,

  Pamela

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  Priyadarshini Thirunavukkarasu

  • November 08, 2021 15:21

  Hello

  Can I use the interval list from this link https://console.cloud.google.com/storage/browser/_details/gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list;tab=live_object

  But, the interval file from the above link has both GRCh38 and Hg19 intervals. Please advice. I want interval list for Genomic build GRCh38

   

  Thanks

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  Pamela Bretscher

  • November 08, 2021 15:29

  Hi Priyadarshini Thirunavukkarasu,

  In the link you shared, I only see the GRCh38 interval lists so this should be what you are looking for. Please let me know if you are seeing an issue when using this interval list.

  Kind regards,

  Pamela

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  Priyadarshini Thirunavukkarasu

  • November 08, 2021 15:51
  • Edited

  I want intervals list for GRCh38. The below excel file was from this link (for GRCh38) but it also shows intervals from Hg19:

  https://console.cloud.google.com/storage/browser/_details/gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list;tab=live_object

  

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  Pamela Bretscher

  • November 08, 2021 18:18

  Hi Priyadarshini Thirunavukkarasu,

  I'm not sure why you are seeing "hg19" in this excel file or where this excel file came from, but the interval lists should be for hg38. Can you find any interval in this file that is only applicable to the hg19 reference build and not hg38? The interval list should work for hg38 and shouldn't have any intervals that are exclusive to hg19.

  Kind regards,

  Pamela

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