Re Dev : To Do

[snewhouse]

New Branch in GIT repn

• [x] make a new branch

f1000_dev on image /home/ubuntu/scratch/ngseasy

Openstack VM

• [x] space
• [x] send key to amos
• [x] 30+ CPU
• [x] max RAM
• [x] Volume : 4TB

Images

• [ ] build images
• [ ] build tool set
• [x] build one image with all tools

Get Genomes

• [x] hg19.fasta
• [x] hs37d5.fasta
• [ ] GRCh38.p7.fasta
• [ ] hs38DH.fasta
• [ ] gatk resources bundles

17.05.2016
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.22_GRCh38.p7/GCA_000001405.22_GRCh38.p7_genomic.fna.gz

Get test data

• [ ] small 30-150x data set

Index Genomes

• [ ] bwa
  • [x] hg19.fasta
  • [x] hs37d5.fasta
  • [ ] hs38DH.fasta
• [ ] snap
  • [ ] hg19.fasta
  • [ ] hs37d5.fasta
  • [ ] hs38DH.fasta
• [ ] novoalign
  • [ ] hg19.fasta
  • [ ] hs37d5.fasta
  • [ ] hs38DH.fasta
• [ ] bowtie2
  • [ ] hg19.fasta
  • [ ] hs37d5.fasta
  • [ ] hs38DH.fasta

bwa

├── hs37d5.fasta
├── hs37d5.fasta.amb
├── hs37d5.fasta.ann
├── hs37d5.fasta.bwt
├── hs37d5.fasta.pac
├── hs37d5.fasta.sa

PLAN BY MONDAY 23rd

giab_data_indexes

https://github.com/genome-in-a-bottle/giab_data_indexes

Test Data

• [ ] 30x Exome
• [ ] 150x Exome
• [ ] 1x WGX at 30x min. (source better WGS data set as X10 is shit and messy)

GATK Gold Standard Run

• [ ] run bwa-realing-bsqr-haplotypecaller on all 3 data sets

This is the "Gold Standard". This will a week if no bugs.

The Glue

Open :-

1. BASH done better than before

• logging
• read a user supplied config file (spreadsheet like)
• user specifies the pipeline
• SJN TO ADD CONFIG PARAMETER LIST
• consider converting to .yaml behind the scenes
• self checks : does input exist move on

RECON BY MONDAY NEXT WEEK

[snewhouse]

hg19
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/

[snewhouse]

https://github.com/lh3/bwa/blob/master/bwakit/run-gen-ref

[snewhouse]

cloned into /home/ubuntu/scratch/ngseasy

[snewhouse]

http://bcb.io/2015/09/17/hg38-validation/

[snewhouse]

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.22_GRCh38.p7/README.txt

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.22_GRCh38.p7/GCA_000001405.22_GRCh38.p7_genomic.fna.gz

[snewhouse]

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa

the readme

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/README.20150309.GRCh38_full_analysis_set_plus_decoy_hla

[snewhouse]

http://biodata.s3-website-us-east-1.amazonaws.com/hg38_bundle/

[snewhouse]

https://github.com/iiiir/GRCH38_gatk_bundle

[snewhouse]

https://github.com/BD2KGenomics/gatk-whole-genome-pipeline/blob/master/GATKsetup.sh

[snewhouse]

https://github.com/BD2KGenomics

[snewhouse]

SJN dev in /mnt/data1/scratch/ngseasy

[snewhouse]

git lfs : https://git-lfs.github.com/

[snewhouse]

cp -v GRCh38_full_analysis_set_plus_decoy_hla.fa GRCh38dH.fasta
'GRCh38_full_analysis_set_plus_decoy_hla.fa' -> 'GRCh38dH.fasta'