Changes between Version 1 and Version 2 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
01/16/14 15:42:38 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling_GATK

    v1 v2  
    1616  * java -jar /usr/local/share/picard-tools/CreateSequenceDictionary.jar R=/path/to/genome/genome.fa O=/path/to/genome/genome.dict
    1717\\
    18 '''Align reads to genome with bwa.'''
     18'''Validate VCF file or known variants''' (with GATK's ValidateVariants)
     19  * java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T ValidateVariants -R /path/to/genome/genome.fa --variant:VCF SNPs_from_NCBI.sorted.vcf \\
     20Respond to errors (by correcting or removing problematic variants), run command again, etc., until validation is successful. \\
     21Otherwise GATK will not run on any subsequent commands that require this file.
     22
     23\\
     24'''Align reads to genome with bwa'''
    1925  * bsub "bwa aln /path/to/genome/bwa/genome Reads_1.fq > Reads_1.sai"
    2026  * bsub "bwa samse /path/to/genome/bwa/genome Reads_1.sai  Reads_1.fq > Reads_1.bwa.sam"
    2127\\
    22 '''Convert SAM to BAM, sort, and index.'''
     28'''Convert SAM to BAM, sort, and index'''
    2329  * bsub /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl Reads_1.bwa.sam
    2430\\