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GRCh38 Reference Name Aliases

Out of date

Please see the updated version of this tutorial.

This should be the content of your "GRCh38.aliases.txt" file.

1	CM000663.2	chr1	NC_000001.11
10	CM000672.2	chr10	NC_000010.11
11	CM000673.2	chr11	NC_000011.10
12	CM000674.2	chr12	NC_000012.12
13	CM000675.2	chr13	NC_000013.11
14	CM000676.2	chr14	NC_000014.9
15	CM000677.2	chr15	NC_000015.10
16	CM000678.2	chr16	NC_000016.10
17	CM000679.2	chr17	NC_000017.11
18	CM000680.2	chr18	NC_000018.10
19	CM000681.2	chr19	NC_000019.10
2	CM000664.2	chr2	NC_000002.12
20	CM000682.2	chr20	NC_000020.11
21	CM000683.2	chr21	NC_000021.9
22	CM000684.2	chr22	NC_000022.11
3	CM000665.2	chr3	NC_000003.12
4	CM000666.2	chr4	NC_000004.12
5	CM000667.2	chr5	NC_000005.10
6	CM000668.2	chr6	NC_000006.12
7	CM000669.2	chr7	NC_000007.14
8	CM000670.2	chr8	NC_000008.11
9	CM000671.2	chr9	NC_000009.12
GL000008.2	chr4_GL000008v2_random	NT_113793.3
GL000009.2	chr14_GL000009v2_random	NT_113796.3
GL000194.1	chr14_GL000194v1_random	NT_113888.1
GL000195.1	chrUn_GL000195v1	NT_113901.1
GL000205.2	chr17_GL000205v2_random	NT_113930.2
GL000208.1	chr5_GL000208v1_random	NT_113948.1
GL000213.1	chrUn_GL000213v1	NT_167208.1
GL000214.1	chrUn_GL000214v1	NT_167209.1
GL000216.2	chrUn_GL000216v2	NT_167211.2
GL000218.1	chrUn_GL000218v1	NT_113889.1
GL000219.1	chrUn_GL000219v1	NT_167213.1
GL000220.1	chrUn_GL000220v1	NT_167214.1
GL000221.1	chr3_GL000221v1_random	NT_167215.1
GL000224.1	chrUn_GL000224v1	NT_167218.1
GL000225.1	chr14_GL000225v1_random	NT_167219.1
GL000226.1	chrUn_GL000226v1	NT_167220.1
KI270302.1	chrUn_KI270302v1	NT_187396.1
KI270303.1	chrUn_KI270303v1	NT_187398.1
KI270304.1	chrUn_KI270304v1	NT_187397.1
KI270305.1	chrUn_KI270305v1	NT_187399.1
KI270310.1	chrUn_KI270310v1	NT_187402.1
KI270311.1	chrUn_KI270311v1	NT_187406.1
KI270312.1	chrUn_KI270312v1	NT_187405.1
KI270315.1	chrUn_KI270315v1	NT_187404.1
KI270316.1	chrUn_KI270316v1	NT_187403.1
KI270317.1	chrUn_KI270317v1	NT_187407.1
KI270320.1	chrUn_KI270320v1	NT_187401.1
KI270322.1	chrUn_KI270322v1	NT_187400.1
KI270329.1	chrUn_KI270329v1	NT_187459.1
KI270330.1	chrUn_KI270330v1	NT_187458.1
KI270333.1	chrUn_KI270333v1	NT_187461.1
KI270334.1	chrUn_KI270334v1	NT_187460.1
KI270335.1	chrUn_KI270335v1	NT_187462.1
KI270336.1	chrUn_KI270336v1	NT_187465.1
KI270337.1	chrUn_KI270337v1	NT_187466.1
KI270338.1	chrUn_KI270338v1	NT_187463.1
KI270340.1	chrUn_KI270340v1	NT_187464.1
KI270362.1	chrUn_KI270362v1	NT_187469.1
KI270363.1	chrUn_KI270363v1	NT_187467.1
KI270364.1	chrUn_KI270364v1	NT_187468.1
KI270366.1	chrUn_KI270366v1	NT_187470.1
KI270371.1	chrUn_KI270371v1	NT_187494.1
KI270372.1	chrUn_KI270372v1	NT_187491.1
KI270373.1	chrUn_KI270373v1	NT_187492.1
KI270374.1	chrUn_KI270374v1	NT_187490.1
KI270375.1	chrUn_KI270375v1	NT_187493.1
KI270376.1	chrUn_KI270376v1	NT_187489.1
KI270378.1	chrUn_KI270378v1	NT_187471.1
KI270379.1	chrUn_KI270379v1	NT_187472.1
KI270381.1	chrUn_KI270381v1	NT_187486.1
KI270382.1	chrUn_KI270382v1	NT_187488.1
KI270383.1	chrUn_KI270383v1	NT_187482.1
KI270384.1	chrUn_KI270384v1	NT_187484.1
KI270385.1	chrUn_KI270385v1	NT_187487.1
KI270386.1	chrUn_KI270386v1	NT_187480.1
KI270387.1	chrUn_KI270387v1	NT_187475.1
KI270388.1	chrUn_KI270388v1	NT_187478.1
KI270389.1	chrUn_KI270389v1	NT_187473.1
KI270390.1	chrUn_KI270390v1	NT_187474.1
KI270391.1	chrUn_KI270391v1	NT_187481.1
KI270392.1	chrUn_KI270392v1	NT_187485.1
KI270393.1	chrUn_KI270393v1	NT_187483.1
KI270394.1	chrUn_KI270394v1	NT_187479.1
KI270395.1	chrUn_KI270395v1	NT_187476.1
KI270396.1	chrUn_KI270396v1	NT_187477.1
KI270411.1	chrUn_KI270411v1	NT_187409.1
KI270412.1	chrUn_KI270412v1	NT_187408.1
KI270414.1	chrUn_KI270414v1	NT_187410.1
KI270417.1	chrUn_KI270417v1	NT_187415.1
KI270418.1	chrUn_KI270418v1	NT_187412.1
KI270419.1	chrUn_KI270419v1	NT_187411.1
KI270420.1	chrUn_KI270420v1	NT_187413.1
KI270422.1	chrUn_KI270422v1	NT_187416.1
KI270423.1	chrUn_KI270423v1	NT_187417.1
KI270424.1	chrUn_KI270424v1	NT_187414.1
KI270425.1	chrUn_KI270425v1	NT_187418.1
KI270429.1	chrUn_KI270429v1	NT_187419.1
KI270435.1	chrUn_KI270435v1	NT_187424.1
KI270438.1	chrUn_KI270438v1	NT_187425.1
KI270442.1	chrUn_KI270442v1	NT_187420.1
KI270448.1	chrUn_KI270448v1	NT_187495.1
KI270465.1	chrUn_KI270465v1	NT_187422.1
KI270466.1	chrUn_KI270466v1	NT_187421.1
KI270467.1	chrUn_KI270467v1	NT_187423.1
KI270468.1	chrUn_KI270468v1	NT_187426.1
KI270507.1	chrUn_KI270507v1	NT_187437.1
KI270508.1	chrUn_KI270508v1	NT_187430.1
KI270509.1	chrUn_KI270509v1	NT_187428.1
KI270510.1	chrUn_KI270510v1	NT_187427.1
KI270511.1	chrUn_KI270511v1	NT_187435.1
KI270512.1	chrUn_KI270512v1	NT_187432.1
KI270515.1	chrUn_KI270515v1	NT_187436.1
KI270516.1	chrUn_KI270516v1	NT_187431.1
KI270517.1	chrUn_KI270517v1	NT_187438.1
KI270518.1	chrUn_KI270518v1	NT_187429.1
KI270519.1	chrUn_KI270519v1	NT_187433.1
KI270521.1	chrUn_KI270521v1	NT_187496.1
KI270522.1	chrUn_KI270522v1	NT_187434.1
KI270528.1	chrUn_KI270528v1	NT_187440.1
KI270529.1	chrUn_KI270529v1	NT_187439.1
KI270530.1	chrUn_KI270530v1	NT_187441.1
KI270538.1	chrUn_KI270538v1	NT_187443.1
KI270539.1	chrUn_KI270539v1	NT_187442.1
KI270544.1	chrUn_KI270544v1	NT_187444.1
KI270548.1	chrUn_KI270548v1	NT_187445.1
KI270579.1	chrUn_KI270579v1	NT_187450.1
KI270580.1	chrUn_KI270580v1	NT_187448.1
KI270581.1	chrUn_KI270581v1	NT_187449.1
KI270582.1	chrUn_KI270582v1	NT_187454.1
KI270583.1	chrUn_KI270583v1	NT_187446.1
KI270584.1	chrUn_KI270584v1	NT_187453.1
KI270587.1	chrUn_KI270587v1	NT_187447.1
KI270588.1	chrUn_KI270588v1	NT_187455.1
KI270589.1	chrUn_KI270589v1	NT_187451.1
KI270590.1	chrUn_KI270590v1	NT_187452.1
KI270591.1	chrUn_KI270591v1	NT_187457.1
KI270593.1	chrUn_KI270593v1	NT_187456.1
KI270706.1	chr1_KI270706v1_random	NT_187361.1
KI270707.1	chr1_KI270707v1_random	NT_187362.1
KI270708.1	chr1_KI270708v1_random	NT_187363.1
KI270709.1	chr1_KI270709v1_random	NT_187364.1
KI270710.1	chr1_KI270710v1_random	NT_187365.1
KI270711.1	chr1_KI270711v1_random	NT_187366.1
KI270712.1	chr1_KI270712v1_random	NT_187367.1
KI270713.1	chr1_KI270713v1_random	NT_187368.1
KI270714.1	chr1_KI270714v1_random	NT_187369.1
KI270715.1	chr2_KI270715v1_random	NT_187370.1
KI270716.1	chr2_KI270716v1_random	NT_187371.1
KI270717.1	chr9_KI270717v1_random	NT_187372.1
KI270718.1	chr9_KI270718v1_random	NT_187373.1
KI270719.1	chr9_KI270719v1_random	NT_187374.1
KI270720.1	chr9_KI270720v1_random	NT_187375.1
KI270721.1	chr11_KI270721v1_random	NT_187376.1
KI270722.1	chr14_KI270722v1_random	NT_187377.1
KI270723.1	chr14_KI270723v1_random	NT_187378.1
KI270724.1	chr14_KI270724v1_random	NT_187379.1
KI270725.1	chr14_KI270725v1_random	NT_187380.1
KI270726.1	chr14_KI270726v1_random	NT_187381.1
KI270727.1	chr15_KI270727v1_random	NT_187382.1
KI270728.1	chr16_KI270728v1_random	NT_187383.1
KI270729.1	chr17_KI270729v1_random	NT_187384.1
KI270730.1	chr17_KI270730v1_random	NT_187385.1
KI270731.1	chr22_KI270731v1_random	NT_187386.1
KI270732.1	chr22_KI270732v1_random	NT_187387.1
KI270733.1	chr22_KI270733v1_random	NT_187388.1
KI270734.1	chr22_KI270734v1_random	NT_187389.1
KI270735.1	chr22_KI270735v1_random	NT_187390.1
KI270736.1	chr22_KI270736v1_random	NT_187391.1
KI270737.1	chr22_KI270737v1_random	NT_187392.1
KI270738.1	chr22_KI270738v1_random	NT_187393.1
KI270739.1	chr22_KI270739v1_random	NT_187394.1
KI270740.1	chrY_KI270740v1_random	NT_187395.1
KI270741.1	chrUn_KI270741v1	NT_187497.1
KI270742.1	chrUn_KI270742v1	NT_187513.1
KI270743.1	chrUn_KI270743v1	NT_187498.1
KI270744.1	chrUn_KI270744v1	NT_187499.1
KI270745.1	chrUn_KI270745v1	NT_187500.1
KI270746.1	chrUn_KI270746v1	NT_187501.1
KI270747.1	chrUn_KI270747v1	NT_187502.1
KI270748.1	chrUn_KI270748v1	NT_187503.1
KI270749.1	chrUn_KI270749v1	NT_187504.1
KI270750.1	chrUn_KI270750v1	NT_187505.1
KI270751.1	chrUn_KI270751v1	NT_187506.1
KI270752.1	chrUn_KI270752v1	NT_187507.1
KI270753.1	chrUn_KI270753v1	NT_187508.1
KI270754.1	chrUn_KI270754v1	NT_187509.1
KI270755.1	chrUn_KI270755v1	NT_187510.1
KI270756.1	chrUn_KI270756v1	NT_187511.1
KI270757.1	chrUn_KI270757v1	NT_187512.1
MT	chrM	J01415.2	NC_012920.1
X	CM000685.2	chrX	NC_000023.11
Y	CM000686.2	chrY	NC_000024.10

For reference, this file was generated by the following script:

getAliases.js
const fetch = require('node-fetch')

async function main() {
  const server = 'https://rest.ensembl.org'
  const ext = '/info/assembly/homo_sapiens'
  const params = 'synonyms=1'
  let response
  try {
    response = await fetch(`${server}${ext}?${params}`, {
      headers: {
        'Content-Type': 'application/json',
      },
    })
  } catch (error) {
    throw new Error(error)
  }
  if (!response.ok) {
    throw new Error(
      `Network response failure: ${response.status} (${response.statusText})`,
    )
  }
  let assemblyInfo
  try {
    assemblyInfo = await response.json()
  } catch (error) {
    throw new Error(error)
  }
  assemblyInfo.top_level_region
    .sort(({ name: a }, { name: b }) => {
      if (a < b) {
        return -1
      }
      if (a > b) {
        return 1
      }
      return 0
    })
    .forEach(region => {
      const synonyms =
        region.synonyms && region.synonyms.map(synonym => synonym.name)
      if (synonyms && synonyms.length) {
        console.log(`${region.name}\t${synonyms.join('\t')}`)
      }
    })
}

main()