= Workflow 1: genome reference file creation = [[TOC()]] 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. - 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 --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 ||