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Created with Raphaël 2.2.05Dec45Nov23Oct121110986543226Sep25241817141331Aug292724232221231Jul3027262524231312327Jun2019187654131May30252_backbone_541.sh: analysis for the backbone_541 to find a SNPmastermaster2_backbone_541.sh: add analysis of backbone_541Merge branch 'master' of gitlab_lbmc:Delattre/JU28_59vs17_SNPchange SNP filtering to use raw SNP in normal conditionREADME.md: update to match the project description1_JU28_59vs17_SNP_calling.sh: change genome ref for intersect_SNP.Rintersect_SNP.R: fix getting sequences partSNP_calling.config: fix module load for SGE1_JU28_59vs17_SNP_calling.sh: add analysis of final_assembly.fasta1_JU28_59vs17_SNP_calling.sh: add PSMN cmdSNP_calling.config: add bioawk for sgeSNP_calling.config: rename some module to loadSNP_calling.nf: add SGE config1_JU28_59vs17_SNP_calling.sh: test of blastSNP_calling.nf: cleanup gatk codeSNP_calling.nf: cleanup bcftools to keep only gatkgatkgatk1_JU28_59vs17_SNP_calling.sh: blast of 5S on the assemblyintersect_SNP.R: add enzyme selectionSNP_calling.nf: fix formatbcftools: add docker file and rm from SAMtools1_JU28_59vs17_SNP_calling.R: add SNP alertintersect_SNP.R: remove printintersect_SNP.R: sort results by AF1_JU28_59vs17_SNP_calling.R: add SNP filtering stepSNP_calling.nf: fix missing report for samtools SNPintersect_SNP.R: add restriction sequenceSNP_calling: add vcf to csv conversion stepintersect_SNP.R: small script to return SNP in arg2 not found in arg1SNP_calling.nf: add SNP calling with bcftoolsSAMTools: add bcftools to the docker imageBowtie2: add sambamba and samblaster to dockerSNP_calling.nf: change RG tag orderSNP_calling.nf: add sample_name info for mapping_fastqSNP_calling.nf: add RG info in bowtie22SNP_calling.nf: change cpus number for bowtieMerge branch 'bwamem'SNP_calling.nf: working pipeline with BWA MEMbwamembwamemSNP_calling.nf: add SNP_filter step1_JU28_59vs17_SNP_calling.nf: fix encoding problem for genomeBioawk: add docker files