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Analysis.md

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MIP Analysis

You can modify all parameters to MIP in order of precedence using:

  1. Command line
  2. Config file
  3. Pedigree file
  4. Definitions file (typically not done by user)

Start standard analysis

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio

--rio means that one block will be performed at the nodes without transfer of files between HDS and SLURM nodes within the block. These block is:

bamcalibrationblock

  • picardtool_mergesamfiles
  • markduplicates
  • gatk_baserecalibration

When not supplying the -rio flag MIP will copy in and out files from HDS and SLURM nodes between each recipe. Thus increasing the network traffic.

Start reannotation and reranking from vcf files

$ mip analyse rd_dna_vcf_rerun [case_id] --config_file [mip_config_rd_dna_vcf_rerun.yaml] --pedigree [case_id_pedigree_vcf_rerun.yaml] --vcf_rerun_file vcf_snv_indel.bcf --sv_vcf_rerun_file vcf_SV.bcf

Excluding a recipe from the analysis

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio --markduplicates 0

Skipping a already processed recipe i.e expect that the ouput has already been generated

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio --markduplicates 2

Simulate standard analysis

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio --dra

-dra means "dry run all" i.e simulation mode. If enabled MIP will execute everything except the final sbatch submission to SLURM and updates to qc_sample_info.yaml.

When not supplying the --dra flag MIP will launch sbatch submission to slurm.

One can use --dra to generate sbatch scripts which then can be submitted manually by the user individually or sequentially using sbatch --dependency=[type]:[jobid]. Note that this will not update qc_sampleInfo.yaml as this is done at MIP run time.

Rerun analysis using exactly the same parameters as last analysis run for case "0"

$ mip analyse rd_dna --config_file 0/analysis/0_config.yaml

Rerun analysis using exactly the same parameters as last analysis run, but in simulation mode

$ mip analyse rd_dna --config_file 0/analysis/0_config.yaml --dra

Turn on individual or consecutive recipes

After performing a dry run all recipes are set to simulation mode in the config. If you want run one or several recipes set them to "1" in the config or supply them on the command line.

$ mip analyse rd_dna --config_file 0/analysis/0_config.yaml --bwa_mem 1 --peddy_ar 1

Run all downstream dependencies starting from a recipe

$ mip analyse rd_dna --config_file 0/analysis/0_config.yaml --start_with_recipe gatk_variantrecalibration

This will swith the mode for all downstream dependencies to run and all recipes upstream of the recipe to simulation mode.

Generate all supported standard recipes

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio --pr

This will print a string with recipes in mode 2 (expect ouput) in chronological order (as far as possible, some things are processed in parallel):

$ mip --split_fastq_file 2 --gzip_fastq 2 --fastqc_ar 2 --bwa_mem 2 --picardtools_mergesamfiles 2 --markduplicates 2 --gatk_baserecalibration 2 --chanjo_sexcheck 2 --sambamba_depth 2 --picardtools_collectmultiplemetrics 2 --picardtools_collecthsmetrics 2 --cnvnator_ar 2 --delly_call 2 --delly_reformat 2 --manta 2 --tiddit 2 --sv_combinevariantcallsets 2 --sv_varianteffectpredictor 2 --sv_vcfparser 2 --sv_rankvariant 2 --sv_reformat 2 --bcftools_mpileup 2 --freebayes_ar 2 --gatk_haplotypecaller 2 --gatk_genotypegvcfs 2 --gatk_variantrecalibration 2 --gatk_combinevariantcallsets 2 --prepareforvariantannotationblock 2 --rhocall_ar 2 --vt_ar 2 --frequency_filter 2 --gatk_variantevalall 2 --gatk_variantevalexome 2 --varianteffectpredictor 2 --vcfparser 2 --snpeff 2 --peddy_ar 2 --plink 2 --variant_integrity_ar 2 --evaluation 2 --rankvariant 2 --endvariantannotationblock 2 --qccollect_ar 2 --multiqc_ar 2 --analysisrunstatus 2 --sacct 2

Thus you will always have the actual recipe names that are supported facilitating starting from any step in the analysis for instance updating qc_sampleInfo.yaml and rerunning recipe in bamcalibrationblock skipping markduplicates:

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio --split_fastq_file 2 --gzip_fastq 2 --fastqc_ar 2 --bwa_mem 2 --picardtools_mergesamfiles 2 --markduplicates 0 --gatk_baserecalibration 2 --chanjo_sexcheck 2 --sambamba_depth 2 --picardtools_collectmultiplemetrics 2 --picardtools_collecthsmetrics 2 --cnvnator_ar 2 --delly_call 2 --delly_reformat 2 --manta 2 --tiddit 2 --sv_combinevariantcallsets 2 --sv_varianteffectpredictor 2 --sv_vcfparser 2 --sv_rankvariant 2 --sv_reformat 2 --bcftools_mpileup 2 --freebayes_ar 2 --gatk_haplotypecaller 2 --gatk_genotypegvcfs 2 --gatk_variantrecalibration 2 --gatk_combinevariantcallsets 2 --prepareforvariantannotationblock 2 --rhocall_ar 2 --vt_ar 2 --frequency_filter 2 --gatk_variantevalall 2 --gatk_variantevalexome 2 --varianteffectpredictor 2 --vcfparser 2 --snpeff 2 --peddy_ar 2 --plink 2 --variant_integrity_ar 2 --evaluation 2 --rankvariant 2 --endvariantannotationblock 2 --qccollect_ar 2 --multiqc 2 --analysisrunstatus 2 --sacct 2

You can of course start or skip any number of recipes as long as it is sane to do so (MIP will not check this but just execute)

You can also modulate the mode of '--pr' using --prm:

$ mip analyse rd_dna [case_id] --config_file [mip_config_rd_dna] --rio --pr --prm 1
$ --split_fastq_file 1 --gzip_fastq 1 --fastqc_ar 1 --bwa_mem 1 --picardtools_mergesamfiles 1 --markduplicates 1 --gatk_baserecalibration 1 --chanjo_sexcheck 1 --sambamba_depth 1 --picardtools_collectmultiplemetrics 1 --picardtools_collecthsmetrics 1 --cnvnator_ar 1 --delly_call 1 --delly_reformat 1 --manta 1 --tiddit 1 --sv_combinevariantcallsets 1 --sv_varianteffectpredictor 1 --sv_vcfparser 1 --sv_rankvariant 1 --sv_reformat 1 --bcftools_mpileup 1 --freebayes_ar 1 --gatk_haplotypecaller 1 --gatk_genotypegvcfs 1 --gatk_variantrecalibration 1 --gatk_combinevariantcallsets 1 --prepareforvariantannotationblock 1 --rhocall_ar 1 --vt_ar 1 --frequency_filter 1 --gatk_variantevalall 1 --gatk_variantevalexome 1 --varianteffectpredictor 1 --vcfparser 1 --snpeff 1 --peddy_ar 1 --plink 1 --variant_integrity_ar 1 --evaluation 1 --rankvariant 1 --endvariantannotationblock 1 --qccollect_ar 1 --multiqc 1 --analysisrunstatus 1 --sacct 1