Ylaine/2009-7-15: Difference between revisions

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  /Users/kunzhang/Downloads/samtools/samtools rmdupse all.sorted.bam all.unique.bam
  /Users/kunzhang/Downloads/samtools/samtools rmdupse all.sorted.bam all.unique.bam
  /Users/kunzhang/Downloads/samtools/samtools pileup -c -f /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined all.unique.bam > all.pileup
  /Users/kunzhang/Downloads/samtools/samtools pileup -c -f /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined all.unique.bam > all.pileup
  /Users/kunzhang/Downloads/samtools/misc/samtools.pl varFilter all.pileup > snp.txt
  /Users/kunzhang/Downloads/samtools/misc/samtools.pl varFilter –D 50000 -d2 all.pileup > snp.txt
  /Users/kunzhang/WorkSpace/Exome/Solexa/scripts/parseExomeCnsSNP.pl /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.seqStartTable.txt snp.txt > snp.chr.txt
  /Users/kunzhang/WorkSpace/Exome/Solexa/scripts/parseExomeCnsSNP.pl /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.seqStartTable.txt snp.txt > snp.chr.txt


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* Try without removing duplicates:
* Try without removing duplicates:
  /Users/kunzhang/Downloads/samtools/samtools pileup -c -f /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined all.sorted.bam > nonunique.pileup
  /Users/kunzhang/Downloads/samtools/samtools pileup -c -f /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined all.sorted.bam > nonunique.pileup
  /Users/kunzhang/Downloads/samtools/misc/samtools.pl varFilter nonunique.pileup > snp.nonunique.txt
  /Users/kunzhang/Downloads/samtools/misc/samtools.pl varFilter –D 50000 -d2 nonunique.pileup > snp.nonunique.txt
/Users/kunzhang/WorkSpace/Exome/Solexa/scripts/parseExomeCnsSNP.pl /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.seqStartTable.txt snp.nonunique.txt > snp.nonunique.chr.txt

Revision as of 20:29, 15 July 2009

Comparing Maq/Maq and Bwa/Sam

Outputs from the two aligning/consensus calling methods often have different read numbers associated with SNPs at the same location, suggesting that the mapping algorithms produce different results. This is confirmed by direct examination of the output 'pileup' files.

  • Run Sam on Maq output. Created new directory "MaqSamTarget"
/Users/kunzhang/Downloads/samtools/misc/maq2sam-long ../MaqTarget/all.map > all.sam
/Users/kunzhang/Downloads/samtools/samtools import /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined.fai all.sam all.bam
/Users/kunzhang/Downloads/samtools/samtools sort all.bam all.sorted
/Users/kunzhang/Downloads/samtools/samtools rmdupse all.sorted.bam all.unique.bam
/Users/kunzhang/Downloads/samtools/samtools pileup -c -f /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined all.unique.bam > all.pileup
/Users/kunzhang/Downloads/samtools/misc/samtools.pl varFilter –D 50000 -d2 all.pileup > snp.txt
/Users/kunzhang/WorkSpace/Exome/Solexa/scripts/parseExomeCnsSNP.pl /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.seqStartTable.txt snp.txt > snp.chr.txt
  • Output is still different from MAQ (lower read numbers)
  • Try without removing duplicates:
/Users/kunzhang/Downloads/samtools/samtools pileup -c -f /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined all.sorted.bam > nonunique.pileup
/Users/kunzhang/Downloads/samtools/misc/samtools.pl varFilter –D 50000 -d2 nonunique.pileup > snp.nonunique.txt
/Users/kunzhang/WorkSpace/Exome/Solexa/scripts/parseExomeCnsSNP.pl /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.seqStartTable.txt snp.nonunique.txt > snp.nonunique.chr.txt