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