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 ftp.completegenomics.com 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:
build37.crr¶
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
Usage¶
Build¶
The build process automatically creates ref/build37.crr and ref/build37.crr.md5 file.