Analysis

Last updated 6 months ago

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 -f 0 -c GRCh37_config_-v1.4-.yaml -rio

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

bamcalibrationblock

  • picardtool_mergesamfiles

  • markduplicates

  • gatk_realignertargetcreator/indelrealigner

  • gatk_baserecalibrator/printreads

variantannotationblock

  • prepareforvariantannotationblock

  • rhocall

  • vt

  • frequency_filter

  • varianteffectpredictor

  • vcfparser

  • snpeff/snpsift

  • rankvariants

  • endvariantannotationblock

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

Excluding a program from the analysis

$ mip -f 0 -c GRCh37_config_-v1.4-.yaml -rio --pMarkduplicates 0

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

$ mip -f 0 -c GRCh37_config_-v1.4-.yaml -rio --pMarkduplicates 2

Simulate standard analysis

$ mip -f 0 -c GRCh37_config_-v1.4-.yaml -rio -dra

-dra means "dry run mode" 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 family 0

$ mip -c 0/analysis/0_config.yaml

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

$ mip -c 0/analysis/0_config.yaml -dra

Turn on individual or consecutive programs

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

$ mip -c 0/analysis/0_config.yaml --pbwa_mem 1 --ppeddy 1

Run all downstream dependencies starting from a program

$ mip -c 0/analysis/0_config.yaml --start_with_program pgatk_variantrecalibration

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

Generate all supported standard programs

$ mip -f 0 -c GRCh37_config_-v1.4-.yaml -rio -pp

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

$ --psplit_fastq_file 2 --pgzip_fastq 2 --pfastqc 2 --pbwa_mem 2 --ppicardtools_mergesamfiles 2 --pmarkduplicates 2 --pgatk_realigner 2 --pgatk_baserecalibration 2 --pchanjo_sexcheck 2 --psambamba_depth 2 --pbedtools_genomecov 2 --ppicardtools_collectmultiplemetrics 2 --ppicardtools_collecthsmetrics 2 --prcovplots 2 --pcnvnator 2 --pdelly_call 2 --pdelly_reformat 2 --pmanta 2 --ptiddit 2 --psv_combinevariantcallsets 2 --psv_varianteffectpredictor 2 --psv_vcfparser 2 --psv_rankvariant 2 --psv_reformat 2 --psamtools_mpileup 2 --pfreebayes 2 --pgatk_haplotypecaller 2 --pgatk_genotypegvcfs 2 --pgatk_variantrecalibration 2 --pgatk_combinevariantcallsets 2 --pprepareforvariantannotationblock 2 --prhocall 2 --pvt 2 --pfrequency_filter 2 --pgatk_variantevalall 2 --pgatk_variantevalexome 2 --pvarianteffectpredictor 2 --pvcfparser 2 --psnpeff 2 --ppeddy 2 --pplink 2 --pvariant_integrity 2 --pevaluation 2 --prankvariant 2 --pendvariantannotationblock 2 --pqccollect 2 --pmultiqc 2 --panalysisrunstatus 2 --psacct 2

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

$ mip -f 0 -c GRCh37_config_-v1.4-.yaml -rio 1 --psplit_fastq_file 2 --pgzip_fastq 2 --pfastqc 2 --pbwa_mem 2 --ppicardtools_mergesamfiles 2 --pmarkduplicates 0 --pgatk_realigner 2 --pgatk_baserecalibration 2 --pchanjo_sexcheck 2 --psambamba_depth 2 --pbedtools_genomecov 2 --ppicardtools_collectmultiplemetrics 2 --ppicardtools_collecthsmetrics 2 --prcovplots 2 --pcnvnator 2 --pdelly_call 2 --pdelly_reformat 2 --pmanta 2 --ptiddit 2 --psv_combinevariantcallsets 2 --psv_varianteffectpredictor 2 --psv_vcfparser 2 --psv_rankvariant 2 --psv_reformat 2 --psamtools_mpileup 2 --pfreebayes 2 --pgatk_haplotypecaller 2 --pgatk_genotypegvcfs 2 --pgatk_variantrecalibration 2 --pgatk_combinevariantcallsets 2 --pprepareforvariantannotationblock 2 --prhocall 2 --pvt 2 --pfrequency_filter 2 --pgatk_variantevalall 2 --pgatk_variantevalexome 2 --pvarianteffectpredictor 2 --pvcfparser 2 --psnpeff 2 --ppeddy 2 --pplink 2 --pvariant_integrity 2 --pevaluation 2 --prankvariant 2 --pendvariantannotationblock 2 --pqccollect 2 --pmultiqc 2 --panalysisrunstatus 2 --psacct 2

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

You can also modulate the mode of '-pp' using -ppm:

$ mip -f 0 -c GRCh37_config_-v1.4-.yaml -rio -pp -ppm 1
$ --psplit_fastq_file 1 --pgzip_fastq 1 --pfastqc 1 --pbwa_mem 1 --ppicardtools_mergesamfiles 1 --pmarkduplicates 1 --pgatk_realigner 1 --pgatk_baserecalibration 1 --pchanjo_sexcheck 1 --psambamba_depth 1 --pbedtools_genomecov 1 --ppicardtools_collectmultiplemetrics 1 --ppicardtools_collecthsmetrics 1 --prcovplots 1 --pcnvnator 1 --pdelly_call 1 --pdelly_reformat 1 --pmanta 1 --ptiddit 1 --psv_combinevariantcallsets 1 --psv_varianteffectpredictor 1 --psv_vcfparser 1 --psv_rankvariant 1 --psv_reformat 1 --psamtools_mpileup 1 --pfreebayes 1 --pgatk_haplotypecaller 1 --pgatk_genotypegvcfs 1 --pgatk_variantrecalibration 1 --pgatk_combinevariantcallsets 1 --pprepareforvariantannotationblock 1 --prhocall 1 --pvt 1 --pfrequency_filter 1 --pgatk_variantevalall 1 --pgatk_variantevalexome 1 --pvarianteffectpredictor 1 --pvcfparser 1 --psnpeff 1 --ppeddy 1 --pplink 1 --pvariant_integrity 1 --pevaluation 1 --prankvariant 1 --pendvariantannotationblock 1 --pqccollect 1 --pmultiqc 1 --panalysisrunstatus 1 --psacct 1