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Get & configure resources (per genome)

Steps

  1. Reference genome
  2. GATK bundle (human only)
  3. dbNSFP database (human only)
  4. Cosmic database (human only)
  5. GoNL database (human only)
  6. Create genome interval list
  7. Create FREEC resource files (human only)
  8. Create resources config

1 Set up reference genome

Download your reference genome of choice from: https://support.illumina.com/sequencing/sequencing_software/igenome.html

wget http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz
tar -xzvf Homo_sapiens_Ensembl_GRCh37.tar.gz

Copy the files in the /Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/* directory to a resources directory:

cp -R /Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/* /nf-iap/resources/GRCh37/Sequence

2 Set up GATK bundle

Download the following files from the GATK bundle for your specific build (in this case GRCh37) :

wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz
wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.idx.gz
wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz
wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.idx.gz
wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz

Copy them to a sensible resources directory. We re-used the directory created in the previous step and copies all files to: /nf-iap/resources/GRCh37/Annotation/. Now unzip all the files and re-zip + index them using the following commands:

gunzip <filename>.vcf.gz
bgzip <filename>.vcf   
tabix <filename>.vcf.gz

3 Set up dbNSFP database

Download the dbNSFP database for your specific build (in this case GRCh37):

wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv2.9.3.zip
unzip dbNSFPv2.9.3.zip

Combine all files and copy the result file to a sensible resources directory. Again we re-used the directory created in step 1 and copied the file to: /nf-iap/resources/GRCh37/Annotation/

(head -n 1 dbNSFP2.9.3_variant.chr1 ; cat dbNSFP2.9.3_variant.chr* | grep -v "^#" ) > dbNSFP2.9.3.txt
bgzip dbNSFP2.9.3.txt
tabix -s 1 -b 2 -e 2 dbNSFP2.9.3.txt.gz

4 Set up COSMIC database

TODO

5 Set up GoNL database

Download all snp_indels files from https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/. Combine all .vcf.gz files together and sort them, we used picard for this (https://gatk.broadinstitute.org/hc/en-us).

wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr1.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr2.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr3.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr4.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr5.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr6.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr7.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr8.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr9.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr10.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr11.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr12.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr13.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr14.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr15.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr16.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr17.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr18.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr19.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr20.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr21.snps_indels.r5.vcf.gz;
wget https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/gonl.chr22.snps_indels.r5.vcf.gz;

java -Xmx4g -jar picard.jar -Djava.io.tmpdir=`pwd`/tmp SortVcf \
      I=gonl.chr1.snps_indels.r5.vcf.gz \
      I=gonl.chr2.snps_indels.r5.vcf.gz \
      I=etc.vcf
      O=gonl.snps_indels.r5.sorted.vcf
      TMP_DIR=`pwd`/tmp
gzip gonl.snps_indels.r5.sorted.vcf

Copy the gonl.snps_indels.r5.sorted.vcf.gz file to /nf-iap/resources/GRCh37/Annotation/.

6 Create genome interval list

If you've download the genome files according to step 1, you can easily create a genome interval list.

awk '{ print $1"\t1\t"$2"\t+\t."}' genome.fa.fai | cat genome.dict - > genome.interval_list

Copy the genome.interval_list to /nf-iap/resources/GRCh37/Sequence/.

7 Create FREEC resource files

Create (or download) a genome.len file. For GRCh37 one is available at http://bioinfo-out.curie.fr/projects/freec/src/hg19.len.

wget http://bioinfo-out.curie.fr/projects/freec/src/hg19.len

Create a directory containing a .fa (fasta) file per chromosome. You can split up the original genome.fa. The human genome the chr_files directory looks like this:

chr_files
      chr1.fa
      chr10.fa
      chr11.fa
      etc

Download and unzip the freec_mappability file.

wget https://xfer.curie.fr/get/nil/7hZIk1C63h0/hg19_len100bp.tar.gz
tar -xzvf https://xfer.curie.fr/get/nil/7hZIk1C63h0/hg19_len100bp.tar.gz

8 Create resources config

Adapt the configs/resources.config file to include the resources you just gathered. Also don't forget to set the resource_dir. An example for human genome build GRCh37 using the files generated in step 1-6:

params {
 resource_dir = '/full/path/to/resources/dir/'
  genomes {
    "GRCh37" {
      fasta = "${params.resource_dir}/GRCh37/Sequence/genome.fa"
      gatk_known_sites = [
        "${params.resource_dir}/GRCh37/Annotation/1000G_phase1.indels.b37.vcf",
        "${params.resource_dir}/GRCh37/Annotation/dbsnp_137.b37.vcf",
        "${params.resource_dir}/GRCh37/Annotation/Mills_and_1000G_gold_standard.indels.b37.vcf"
      ]
      dbsnp = "${params.resource_dir}/GRCh37/Annotation/dbsnp_137.b37.vcf"
      dbnsfp = "${params.resource_dir}/GRCh37/Annotation/dbNSFP2.9.3_variant.txt.gz"
      cosmic = "${params.resource_dir}/GRCh37/Annotation/CosmicCodingMuts_v76.vcf.gz"
      gonl = "${params.resource_dir}/GRCh37/Annotation/gonl.snps_indels.r5.sorted.vcf"
      interval_list = "${params.resource_dir}/GRCh37/Sequence/genome.interval_list"
      freec_chr_len = "${params.resource_dir}/GRCh37/Sequence/genome.len"
      freec_chr_files = "${params.resource_dir}/GRCh37/Sequence/chr_files"
      freec_mappability = "${params.resource_dir}/GRCh37/Annotation/misc/out100m2_hg19.gem"
    }
  }
}