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Generating Complete Genomics build37 Files

As part of the TARGET AML Data Analysis project I was working on to support my wife's research, I found myself analyzing Complete Genomics produced gene sequences.

As the sequences were produced in the early 2010's, CGI did not provide a complete set of .vcf files.

Creating .vcf files from the provided input requires using the cgatools mkvcf command.

At the time of development, the CGI reference sequences hosted on were unaccessible, therefore, the required inputs for cgatools mkvcf needed to be created using the process described in the CGAtools 1.8 User Guide (pages 16-18).

The cgatools documentation mentions two mythical files, build37.crr and build37.fa, required to utilize the tool. The provided documentation advices retrieving the files from an FTP site which no longer exists.

Therefore, I had to figure out how to generate these files myself.

The fruits of this effort are the following repositories:


This Dockerfile automatically generates a build37.crr reference file to support analyzing Complete Genomics Incorporated (CGI) sequencing data.

The generated build37.crr matches the CGI reference build37.crr file:

> cgatools listcrr --reference ref/build37.crr
ChromosomeId Chromosome    Length Circular Md5
   0       chr1 249250621    false 1b22b98cdeb4a9304cb5d48026a85128
   1       chr2 243199373    false a0d9851da00400dec1098a9255ac712e
   2       chr3 198022430    false 641e4338fa8d52a5b781bd2a2c08d3c3
   3       chr4 191154276    false 23dccd106897542ad87d2765d28a19a1
   4       chr5 180915260    false 0740173db9ffd264d728f32784845cd7
   5       chr6 171115067    false 1d3a93a248d92a729ee764823acbbc6b
   6       chr7 159138663    false 618366e953d6aaad97dbe4777c29375e
   7       chr8 146364022    false 96f514a9929e410c6651697bded59aec
   8       chr9 141213431    false 3e273117f15e0a400f01055d9f393768
   9      chr10 135534747    false 988c28e000e84c26d552359af1ea2e1d
  10      chr11 135006516    false 98c59049a2df285c76ffb1c6db8f8b96
  11      chr12 133851895    false 51851ac0e1a115847ad36449b0015864
  12      chr13 115169878    false 283f8d7892baa81b510a015719ca7b0b
  13      chr14 107349540    false 98f3cae32b2a2e9524bc19813927542e
  14      chr15 102531392    false e5645a794a8238215b2cd77acb95a078
  15      chr16  90354753    false fc9b1a7b42b97a864f56b348b06095e6
  16      chr17  81195210    false 351f64d4f4f9ddd45b35336ad97aa6de
  17      chr18  78077248    false b15d4b2d29dde9d3e4f93d1d0f2cbc9c
  18      chr19  59128983    false 1aacd71f30db8e561810913e0b72636d
  19      chr20  63025520    false 0dec9660ec1efaaf33281c0d5ea2560f
  20      chr21  48129895    false 2979a6085bfe28e3ad6f552f361ed74d
  21      chr22  51304566    false a718acaa6135fdca8357d5bfe94211dd
  22       chrX 155270560    false 7e0e2e580297b7764e31dbc80c2540dd
  23       chrY  59373566    false 1e86411d73e6f00a10590f976be01623
  24       chrM     16569     true c68f52674c9fb33aef52dcf399755519

Pasted image 20230328225308.png - CGA Tools User Guide 1.8



The build process automatically creates ref/build37.crr and ref/build37.crr.md5 file.




# Confirm the generated build37.crr file matches the CGI reference file
cgatools listcrr --reference ref/build37.crr

# Copy the generated build37.crr out of the container
cp ref/build37.crr output/

Last update: 2023-03-28