VCF UNIQ DECOMPOSITION

cd /Bioinformatics/Users/zfu/2015_Nadine_Strep

/Bioinformatics/Users/zfu/packages/vt/vt decompose ./9-1/03.Freebayes/9-1_sorted.vcf -o ./9-1/03.Freebayes/9-1.decomposed.vcf

/Bioinformatics/Users/zfu/packages/vt/vt normalize ./9-1/03.Freebayes/9-1.decomposed.vcf -r ./00.RawData/Strep.fasta | /Bioinformatics/Users/zfu/packages/vt/vt uniq - -o ./9-1/03.Freebayes/9-1.normalized_uniq.vcf

/Bioinformatics/Users/zfu/packages/vt/vt decompose_blocksub ./9-1/03.Freebayes/9-1.normalized_uniq.vcf -o ./9-1/03.Freebayes/9-1.decomposed_blocksub.vcf

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/Bioinformatics/Users/zfu/packages/freebayes/bin/freebayes -F 0.01 -p 1 --fasta-reference /Bioinformatics/Users/zfu/2015_Stephanie_BAC/00.RawData/clone.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/04.Clone/2014_clone_sorted.bam > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/06.Freebayes/2014_clone_sorted.vcf

/Bioinformatics/Users/zfu/packages/vcflib/bin/vcffilter -f "QUAL > 20" /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/06.Freebayes/2014_clone_sorted.vcf > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/06.Freebayes/2014_clone_filtered.vcf

cd /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/src/

python generateConsensusData_Ori.py ../06.Freebayes/2014_clone_sorted.vcf ../../00.RawData/oneLine.fasta/clone_oneLine.fasta ../07.Consensus.Fasta/2014_clone_Consensus.fa ../07.Consensus.Fasta/2014_clone_noGap_Consensus.fa  ../06.Freebayes/2014_clone_snpInfo.tsv


python generateConsensusData_Freq.py ../06.Freebayes/2014_clone_filtered.vcf ../../00.RawData/oneLine.fasta/clone_oneLine.fasta ../07.Consensus.Fasta/2014_clone_Consensus.filtered.fa ../07.Consensus.Fasta/2014_clone_noGap_Consensus.filtered.fa  ../06.Freebayes/2014_clone_snpInfo.filtered.tsv ../06.Freebayes/2014_clone_snpInfo.filtered_Freq.vcf