Changes between Initial Version and Version 1 of AlleleCounting


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Timestamp:
Aug 24, 2011 10:47:16 AM (13 years ago)
Author:
Morris Swertz
Comment:

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  • AlleleCounting

    v1 v1  
     1= Allele Counting SOP =
     2
     3This method can be used to create a SNP list across multiple samples and establish the allele count for each variant.
     4
     5== Step 1: Merge samples vcf using GATK CombineVariants ==
     6
     7Merge sample vcf using [http://www.broadinstitute.org/gsa/wiki/index.php/CombineVariants CombineVariants]
     8Semi-code:
     9{{{
     10cd ~/projects/yourproject/rawdata
     11java -Xmx2g -jar /target/gpfs2/gcc/tools/GATK-1.1-23-g8072bd9/Sting/dist/GenomeAnalysisTK.jar\
     12 -T CombineVariants\
     13 -B:sample1,VCF sample1.all.snp.txt.vcf\
     14 -B:sample2,VCF sample2.all.snp.txt.vcf\
     15 -B:sample3,VCF sample3.all.snp.txt.vcf\
     16 -B:sample4,VCF sample4.all.snp.txt.vcf\
     17 -R /target/gpfs2/gcc/resources/hg19/indices/hg19.fa\
     18 -o union.vcf
     19}}}
     20
     21== Step 2: count alleles using VCF tools ==
     22
     23TODO