snps calling

/Bioinformatics/Users/zfu/packages/freebayes/bin/freebayes -F 0.01 -p 1 --fasta-reference /Bioinformatics/Users/zfu/2015_Stephanie_BAC/00.RawData/clone_GFP.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/05.Clone_GFP/L80_clone_GFP_sorted.bam > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_sorted.vcf

/Bioinformatics/Users/zfu/packages/vcflib/bin/vcffilter -f "QUAL > 20" /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_sorted.vcf > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_filtered.vcf

cd /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L51/src/

python generateConsensusData_Ori.py /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_sorted.vcf /Bioinformatics/Users/zfu/2015_Stephanie_BAC/00.RawData/oneLine.fasta/clone_oneLine_GFP.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/07.Consensus.Fasta/L80_clone_GFP_Consensus.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/07.Consensus.Fasta/L80_clone_GFP_Consensus_noGap.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_snpInfo.tsv

python generateConsensusData_Freq.py /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_filtered.vcf /Bioinformatics/Users/zfu/2015_Stephanie_BAC/00.RawData/oneLine.fasta/clone_oneLine_GFP.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/07.Consensus.Fasta/L80_clone_GFP_Consensus.filtered.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/07.Consensus.Fasta/L80_clone_GFP_Consensus_noGap.filtered.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_snpInfo.filtered.tsv /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/06.Freebayes/L80_clone_GFP_snpInfo_filtered_Freq.vcf