Ylaine/2009-7-15
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Maq/Sam
Outputs from the two aligning/consensus calling methods (Maq/Maq and Bwa/Sam) 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
- Read numbers tend to be +1 higher than for Maq/Maq
- Found 24532 SNPs (vs 8376 for Maq easyrun)
- SNPs for which Maq reported a depth of 255 reads are missing altogether from Maq/Sam