wiki:SnpCallingPipeline/ReferencePreparation

Workflow 1: genome reference file creation

This workflow creates reference files per chromosome including:

  • genome, dbsnp and indel vcfs per chromosome
  • realign targets for faster realignment target creation
  • index files for samtools and bwa

Workflow inputs:

  • genome.chr.fa - downloaded from genome supplier (now hg19)
  • dbsnpXYZ.rod - downloaded reference SNPs from dbsnp (now 129)
  • indelsXYZ.vcf - downloaded reference indels from 1KG

Workflow outputs:

  • genome.chr.fa - cleaned headers
  • genome.chr.fa.fa - index for samtools
  • genome.chr.fa.<format> - multilple index files for bwa
  • dbsnpXYZ.chr.rod - split per chromosome
  • indelsXYZ.chr.vcf - split per chromosome
  • genome.chr.realign.intervals - targets for realignment

clean-fasta-headers

Clean headers to only have '1' instead of Chr1, etc

tool:
inputs: genome.chr.fa
outputs: genome.chr.fa
doc: internally developed

split-vcf-chr for dbsnp and indels

Split vcf per chromosome

tool:
inputs: dbsnpXYZ.rod, indelsXYZ.vcf
outputs: dbsnpXYz.chr.rod, indelsXYZ.vcf
doc:

Discussion:

Can we use http://vcftools.sourceforge.net/options.html ?

vcftools --vcf indelsXYZ.vcf --chr <i> --recode --out indelsXYZ.chr

index-chromosomes

Index reference sequence for each chromosome in the FASTA format

tool: samtools faidx
input: genome.chr.fa
output: genome.chr.fa.fai
doc: http://samtools.sourceforge.net/samtools.shtml#3

bwa-index-chromosomes

Index reference sequence for each chromosome for bwa alignment

tool: bwa index -a IS
input: genome.chr.fa
output: genome.chr.fa.xyz
doc: http://bio-bwa.sourceforge.net/bwa.shtml#3

RealignerTargetCreator

Generate realignment targets for known sites for each chromosome

tool: GenomeAnalysisTK.jar -T RealignerTargetCreator?
input: genome.chr.fa, dbsnpXYz.chr.rod, indelsXYZ.vcf
output: genome.chr.realign.intervals
doc: http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites
Last modified 7 years ago Last modified on Oct 18, 2010 4:46:17 AM