Changes between Version 42 and Version 43 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 18, 2010 4:45:34 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v42 v43  
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    78 
    79 == Workflow 1: genome reference file creation ==
    80 
    81 This workflow creates reference files per chromosome including:
    82 * genome, dbsnp and indel vcfs per chromosome
    83 * realign targets for faster realignment target creation
    84 * index files for samtools and bwa
    85 
    86 Workflow inputs:
    87 * genome.chr.fa - downloaded from genome supplier (now hg19)
    88 * dbsnpXYZ.rod - downloaded reference SNPs from dbsnp (now 129)
    89 * indelsXYZ.vcf - downloaded reference indels from 1KG
    90 
    91 Workflow outputs:
    92 * genome.chr.fa - cleaned headers
    93 * genome.chr.fa.fa - index for samtools
    94 * genome.chr.fa.<format> - multilple index files for bwa
    95 * dbsnpXYZ.chr.rod - split per chromosome
    96 * indelsXYZ.chr.vcf - split per chromosome
    97 * genome.chr.realign.intervals - targets for realignment
    98 
    99 === clean-fasta-headers ===
    100 Clean headers to only have '1' instead of Chr1, etc
    101 
    102 ||tool:    || ||
    103 ||inputs:  ||genome.chr.fa ||
    104 ||outputs: ||genome.chr.fa ||
    105 ||doc:     ||internally developed ||
    106 
    107 === split-vcf-chr for dbsnp and indels ===
    108 Split vcf per chromosome
    109 ||tool:    || ||
    110 ||inputs:  ||dbsnpXYZ.rod, indelsXYZ.vcf ||
    111 ||outputs: ||dbsnpXYz.chr.rod, indelsXYZ.vcf ||
    112 ||doc:     || ||
    113 
    114 Discussion:
    115 > Can we use http://vcftools.sourceforge.net/options.html ?
    116 >> vcftools --vcf indelsXYZ.vcf --chr <i> --recode --out indelsXYZ.chr
    117 
    118 === index-chromosomes ===
    119 Index reference sequence for each chromosome in the FASTA format
    120 
    121 ||tool:   ||samtools faidx ||
    122 ||input:  ||genome.chr.fa ||
    123 ||output: ||genome.chr.fa.fai ||
    124 ||doc:    ||http://samtools.sourceforge.net/samtools.shtml#3 ||
    125 
    126 === bwa-index-chromosomes ===
    127 Index reference sequence for each chromosome for bwa alignment
    128 
    129 ||tool:   ||bwa index -a IS ||
    130 ||input:  ||genome.chr.fa ||
    131 ||output: ||genome.chr.fa.xyz ||
    132 ||doc:    ||http://bio-bwa.sourceforge.net/bwa.shtml#3 ||
    133 
    134 === !RealignerTargetCreator ===
    135 Generate realignment targets for known sites for each chromosome
    136 
    137 ||tool:   ||GenomeAnalysisTK.jar -T RealignerTargetCreator ||
    138 ||input:  ||genome.chr.fa, dbsnpXYz.chr.rod, indelsXYZ.vcf ||
    139 ||output: ||genome.chr.realign.intervals ||
    140 ||doc:    ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites ||
    141 
    142