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Last update: 20250102

Design release DNA SNV INDEL v1

Protocol name: design_dna_snv_indel_v1_relsease (this document) for design_dna_snvindel_v1 (see design_dna_snvindel_v1).

Release information

Current release version: v1
Location temp: /project/data/shared_all/release_dna_snv_indel_v1
Location stable: /project/data/shared/release_dna_snv_indel_v1

Status

Status: design_dna_snv_indel_v2_relsease is currently recommended.
We have added new annotation settings affecting which QV are reported.
Any modifications due to error will be notified and a new release ID will be issued (e.g. design_dna_snv_indel_v1.2_relsease).

About

If you are reading this then you are interested in using the release data from the design_dna_snvindel_v1 pipeline. This pipeline produces a multi-use dataset via the qualifying variants 1 (QV1) protocol. Incremental additions with new data for this release will be added. Potential uses are suggested as the end-points in figure 1 (e.g. statistical genomics, etc.)

The protocol used was:

  1. design_dna_snvindel_v1

Figure 1: Summary of design DNA SNV INDEL v1 pipeline plan.

Contents

See the README.md for this release to find files:

dna_snv_indel_v1_release.README.md

Data synchronisation process

  1. Sync release data to shared_all.
  2. Log and verify data during sync to shared_all.
  3. Data manager syncs from shared_all to shared.
  4. The final release is locked in shared but allows incremental additions.
  5. Labelled as release_dna_snv_indel_v1.

Data Availability

All raw and processed data are accessible to all internal researchers. Processed/intermediate data might change during projects, so released data is recommended for downstream projects. Release data should have detailed supporting documentation following the protocol. Essential data is curated to minimise storage use. Non-release data is accessible as usual from user directories but may be overwritten or updated without notice. Data paths are listed in the release script, generally read from a master list of variables.

Current version script

release_dna_snv_indel_v1.sh is run from the user src directory.

Checksums

All files are logged with their md5 checksum. To verify integrity run: md5sum -c checksums.md5

$ cat checksums.md5
457dc93749669bed628575dfe551bdac  ./release_dna_snv_indel_v1.sh.log
d35670b5ac26302b19f07c4cf3a96977  ./release_dna_snv_indel_v1.out

$ md5sum -c checksums.md5
./release_dna_snv_indel_v1.sh.log: OK
./release_dna_snv_indel_v1.out: OK

Stats

Chromosome 1
Number of samples: 180
Number of SNPs:    1543167
Number of INDELs:  385213
Number of MNPs:    0
Number of others:  0
Number of sites:   1972696

Chromosome 2
Number of samples: 180
Number of SNPs:    1620394
Number of INDELs:  394968
Number of MNPs:    0
Number of others:  0
Number of sites:   2061648

Chromosome 3
Number of samples: 180
Number of SNPs:    1316780
Number of INDELs:  324975
Number of MNPs:    0
Number of others:  0
Number of sites:   1673128

Chromosome 4
Number of samples: 180
Number of SNPs:    1337064
Number of INDELs:  316959
Number of MNPs:    0
Number of others:  0
Number of sites:   1689336

Chromosome 5
Number of samples: 180
Number of SNPs:    1196261
Number of INDELs:  293793
Number of MNPs:    0
Number of others:  0
Number of sites:   1520849

Chromosome 6
Number of samples: 180
Number of SNPs:    1214390
Number of INDELs:  303459
Number of MNPs:    0
Number of others:  0
Number of sites:   1552036

Chromosome 7
Number of samples: 180
Number of SNPs:    1145244
Number of INDELs:  277881
Number of MNPs:    0
Number of others:  0
Number of sites:   1460406

Chromosome 8
Number of samples: 180
Number of SNPs:    1020218
Number of INDELs:  240781
Number of MNPs:    0
Number of others:  0
Number of sites:   1284467

Chromosome 9
Number of samples: 180
Number of SNPs:    858094
Number of INDELs:  198839
Number of MNPs:    0
Number of others:  0
Number of sites:   1080126

Chromosome 10
Number of samples: 180
Number of SNPs:    946539
Number of INDELs:  237079
Number of MNPs:    0
Number of others:  0
Number of sites:   1212448

Chromosome 11
Number of samples: 180
Number of SNPs:    910215
Number of INDELs:  221252
Number of MNPs:    0
Number of others:  0
Number of sites:   1154276

Chromosome 12
Number of samples: 180
Number of SNPs:    903797
Number of INDELs:  242211
Number of MNPs:    0
Number of others:  0
Number of sites:   1173553

Chromosome 13
Number of samples: 180
Number of SNPs:    683880
Number of INDELs:  169236
Number of MNPs:    0
Number of others:  0
Number of sites:   872669

Chromosome 14
Number of samples: 180
Number of SNPs:    618962
Number of INDELs:  156463
Number of MNPs:    0
Number of others:  0
Number of sites:   792576

Chromosome 15
Number of samples: 180
Number of SNPs:    609207
Number of INDELs:  141670
Number of MNPs:    0
Number of others:  0
Number of sites:   768672

Chromosome 16
Number of samples: 180
Number of SNPs:    653752
Number of INDELs:  151086
Number of MNPs:    0
Number of others:  0
Number of sites:   826293

Chromosome 17
Number of samples: 180
Number of SNPs:    521864
Number of INDELs:  161194
Number of MNPs:    0
Number of others:  0
Number of sites:   700410

Chromosome 18
Number of samples: 180
Number of SNPs:    534571
Number of INDELs:  130405
Number of MNPs:    0
Number of others:  0
Number of sites:   680157

Chromosome 19
Number of samples: 180
Number of SNPs:    455618
Number of INDELs:  136628
Number of MNPs:    0
Number of others:  0
Number of sites:   610238

Chromosome 20
Number of samples: 180
Number of SNPs:    427477
Number of INDELs:  108222
Number of MNPs:    0
Number of others:  0
Number of sites:   547588

Chromosome 21
Number of samples: 180
Number of SNPs:    333850
Number of INDELs:  67464
Number of MNPs:    0
Number of others:  0
Number of sites:   413496

Chromosome 22
Number of samples: 180
Number of SNPs:    332138
Number of INDELs:  74089
Number of MNPs:    0
Number of others:  0
Number of sites:   418913

Chromosome X
Number of samples: 180
Number of SNPs:    678392
Number of INDELs:  183618
Number of MNPs:    0
Number of others:  0
Number of sites:   881808

Chromosome Y
Number of samples: 180
Number of SNPs:    71640
Number of INDELs:  1289
Number of MNPs:    0
Number of others:  0
Number of sites:   77666