Config¶
The VIP configuration is stored in Nextflow configuration files. An additional configuration file can be supplied on the command-line to overwrite default parameter values, add/update profiles, configure processes and update environment variables.
Parameters¶
| key | default | description |
|---|---|---|
| assembly | GRCh38 | output assembly, allowed values: [GRCh38] |
| GRCh37.reference.chain.GRCh38 | installed | chain file to convert GRCh37 to GRCh38 data |
| GRCh37.reference.fasta | installed | |
| GRCh37.reference.fastaFai | installed | |
| GRCh37.reference.fastaGzi | installed | |
| GRCh38.reference.fasta | installed | GCA_000001405.15_GRCh38_no_alt_analysis_set |
| GRCh38.reference.fastaFai | installed | |
| GRCh38.reference.fastaGzi | installed | |
| T2T.reference.chain.GRCh38 | installed | chain file to convert T2T to GRCh38 data |
| T2T.reference.fasta | ||
| T2T.reference.fastaFai | ||
| T2T.reference.fastaGzi | ||
| pcr_performed | false | Indication if PCR was performed to get the data, if so certain tools will be disabled due to not being compatible with this data. |
Warning: Please take note of the fact that for a different reference fasta.gz the unzipped referenfasta file is also required. Both the zipped and unzipped fasta should have an index.
FASTQ¶
| key | default | description |
|---|---|---|
| GRCh38.reference.fastaMmi | installed | for details, see here |
| fastp.options | for details, see here | |
| minimap2.soft_clipping | true | In SAM output, use soft clipping for supplementary alignments (required when STR calling with Straglr) |
| minimap2.nanopore_preset | lr:hq | Preset to use for aligning Nanopore data, options: 'lr:hq' 'map-ont'. |
CRAM¶
| key | default | description |
|---|---|---|
| cnv.spectre.GRCh38.blacklist | installed | blacklist in bed format for sites that will be ignored |
| cnv.spectre.GRCh38.metadata | installed | metadata file for Ns removal, update this file only when using a different GRCh38 version than the one provided by VIP. |
| cram.call_snv | true | enable/disable the detection of short variants |
| cram.call_str | true | enable/disable the detection of short tandem repeats |
| cram.call_sv | true | enable/disable the detection of structural variants. disable this manually in case of non-paired-end Illumina data. |
| snv.deeptrio.illumina.WES.model_name | WES | for details, see here |
| snv.deeptrio.illumina.WGS.model_name | WGS | for details, see here |
| snv.deeptrio.nanopore.model_name | ONT | for details, see here |
| snv.deeptrio.pacbio_hifi.model_name | PACBIO | for details, see here |
| snv.deepvariant.illumina.WES.model_name | WES | for details, see here |
| snv.deepvariant.illumina.WGS.model_name | WGS | for details, see here |
| snv.deepvariant.nanopore.model_name | ONT_R104 | for details, see here |
| snv.deepvariant.pacbio_hifi.model_name | PACBIO | for details, see here |
| snv.glnexus.WES.preset | DeepVariantWES | for details, see here. allowed values: [DeepVariant, DeepVariantWES, DeepVariantWES_MED_DP, DeepVariant_unfiltered] |
| snv.glnexus.WGS.preset | DeepVariantWGS | for details, see here. allowed values: [DeepVariant, DeepVariantWGS, DeepVariant_unfiltered] |
| str.expansionhunter.aligner | dag-aligner | for details, see here. allowed values: [dag-aligner, path-aligner] |
| str.expansionhunter.analysis_mode | streaming | for details, see here. allowed values: [seeking , streaming] |
| str.expansionhunter.log_level | warn | for details, see here. allowed values: [trace, debug, info, warn, or error] |
| str.expansionhunter.region_extension_length | 1000 | for details, see here |
| str.expansionhunter.GRCh38.variant_catalog | installed | for details, see here |
| str.straglr.min_support | 2 | minimum number of support reads for an expansion to be captured in genome-scan, see here |
| str.straglr.min_cluster_size | 2 | minimum number of reads required to constitute a cluster (allele) in GMM clustering, see here |
| str.straglr.GRCh38.loci | installed | from here |
| sv.cutesv.batches | 10000000 | Batch of genome segmentation interval |
| sv.cutesv.gt_round | 500 | Maximum round of iteration for alignments searching if perform genotyping |
| sv.cutesv.include_bed | Only detect SVs in regions in the BED file | |
| sv.cutesv.ivcf | Enable to perform force calling using the given vcf file | |
| sv.cutesv.max_size | 100000 | Maximum size of SV to be reported. All SVs are reported when using -1 |
| sv.cutesv.max_split_parts | 7 | Maximum number of split segments a read may be aligned before it is ignored. All split segments are considered when using -1. (Recommand -1 when applying assembly-based alignment.) |
| sv.cutesv.merge_del_threshold | 0 | Maximum distance of deletion signals to be merged |
| sv.cutesv.merge_ins_threshold | 100 | Maximum distance of insertion signals to be merged |
| sv.cutesv.min_mapq | 20 | Minimum mapping quality value of alignment to be taken into account (recommend 10 for force calling) |
| sv.cutesv.min_read_len | 500 | Ignores reads that only report alignments with not longer than bp |
| sv.cutesv.min_siglength | 10 | Minimum length of SV signal to be extracted |
| sv.cutesv.min_size | 30 | Minimum size of SV to be reported |
| sv.cutesv.min_support | 10 | Minimum number of reads that support a SV to be reported |
| sv.cutesv.read_range | 1000 | The interval range for counting reads distribution |
| sv.cutesv.report_readid | false | Enable to report supporting read ids for each SV |
| sv.cutesv.retain_work_dir | false | Enable to retain temporary folder and files |
| sv.cutesv.write_old_sigs | false | Enable to output temporary sig files |
| sv.cutesv.nanopore.diff_ratio_filtering_TRA | 0.6 | Filter breakpoints with basepair identity less than |
| sv.cutesv.nanopore.diff_ratio_merging_DEL | 0.3 | Do not merge breakpoints with basepair identity more than |
| sv.cutesv.nanopore.diff_ratio_merging_INS | 0.3 | Do not merge breakpoints with basepair identity more than |
| sv.cutesv.nanopore.max_cluster_bias_DEL | 100 | Maximum distance to cluster read together for deletion |
| sv.cutesv.nanopore.max_cluster_bias_DUP | 500 | Maximum distance to cluster read together for duplication |
| sv.cutesv.nanopore.max_cluster_bias_INS | 100 | Maximum distance to cluster read together for insertion |
| sv.cutesv.nanopore.max_cluster_bias_INV | 500 | Maximum distance to cluster read together for inversion |
| sv.cutesv.nanopore.max_cluster_bias_TRA | 50 | Maximum distance to cluster read together for translocation |
| sv.cutesv.nanopore.remain_reads_ratio | 1.0 | The ratio of reads remained in cluster. Set lower when the alignment data have high quality but recommand over 0.5 |
| sv.cutesv.pacbio_hifi.diff_ratio_filtering_TRA | 0.6 | Filter breakpoints with basepair identity less than |
| sv.cutesv.pacbio_hifi.diff_ratio_merging_DEL | 0.5 | Do not merge breakpoints with basepair identity more than |
| sv.cutesv.pacbio_hifi.diff_ratio_merging_INS | 0.9 | Do not merge breakpoints with basepair identity more than |
| sv.cutesv.pacbio_hifi.max_cluster_bias_DEL | 1000 | Maximum distance to cluster read together for deletion |
| sv.cutesv.pacbio_hifi.max_cluster_bias_DUP | 500 | Maximum distance to cluster read together for duplication |
| sv.cutesv.pacbio_hifi.max_cluster_bias_INS | 1000 | Maximum distance to cluster read together for insertion |
| sv.cutesv.pacbio_hifi.max_cluster_bias_INV | 500 | Maximum distance to cluster read together for inversion |
| sv.cutesv.pacbio_hifi.max_cluster_bias_TRA | 50 | Maximum distance to cluster read together for translocation |
| sv.cutesv.pacbio_hifi.remain_reads_ratio | 1.0 | The ratio of reads remained in cluster. Set lower when the alignment data have high quality but recommand over 0.5 |
gVCF¶
| key | default | description |
|---|---|---|
| gvcf.merge_preset | DeepVariant | allowed values: [gatk, gatk_unfiltered, DeepVariant, DeepVariant_unfiltered] |
VCF¶
| key | default | description |
|---|---|---|
| vcf.start | allowed values: [normalize, annotate, classify, filter, inheritance, classify_samples, filter_samples]. for reanalysis this defines from which step to start the workflow | |
| vcf.annotate.annotsv_cache_dir | installed | |
| vcf.annotate.ensembl_gene_mapping | installed | |
| vcf.annotate.vep_buffer_size | 1000 | for details, see here |
| vcf.annotate.vep_cache_dir | installed | |
| vcf.annotate.vep_plugin_dir | installed | |
| vcf.annotate.vep_plugin_hpo | installed | |
| vcf.annotate.vep_plugin_inheritance | installed | |
| vcf.annotate.vep_plugin_vkgl_mode | 1 | allowed values: [0=full VKGL, 1=public VKGL]. update vcf.annotate.GRCh38.vep_plugin_vkgl accordingly |
| vcf.annotate.GRCh38.capice_model | installed | |
| vcf.annotate.GRCh38.vep_custom_phylop | installed | |
| vcf.annotate.GRCh38.vep_plugin_clinvar | installed | |
| vcf.annotate.GRCh38.vep_plugin_gnomad | installed | |
| vcf.annotate.GRCh38.vep_plugin_green_db_enabled | false | enabling is only allowed for academic use, for details see here |
| vcf.annotate.GRCh38.vep_plugin_green_db | installed | |
| vcf.annotate.GRCh38.vep_plugin_spliceai_indel | installed | |
| vcf.annotate.GRCh38.vep_plugin_spliceai_snv | installed | |
| vcf.annotate.GRCh38.vep_plugin_utrannotator | installed | |
| vcf.annotate.GRCh38.vep_plugin_vkgl | installed | update vcf.annotate.vep_plugin_vkgl_mode accordingly |
| vcf.classify.annotate_path | 1 | allowed values: [0=false, 1=true]. annotate variant-consequences with classification tree path |
| vcf.classify.GRCh38.decision_tree | installed | for details, see here |
| vcf.classify_samples.annotate_path | 1 | allowed values: [0=false, 1=true]. annotate variant-consequences per sample with classification tree path |
| vcf.classify_samples.GRCh38.decision_tree | installed | for details, see here |
| vcf.filter.classes | VUS,LP,P | for details, see here |
| vcf.filter.consequences | true | allowed values: [true, false]. true: filter individual consequences, false: keep all consequences for a variant if one consequence filter passes. |
| vcf.filter_samples.classes | U1,U2 | for details, see here |
| vcf.report.gado_genes | installed | |
| vcf.report.gado_hpo | installed | |
| vcf.report.gado_predict_info | installed | |
| vcf.report.gado_predict_matrix | installed | |
| vcf.report.include_crams | true | allowed values: [true, false]. true: include cram files in the report for showing alignments in the genome browser, false: do not include the crams in the report, no aligments are shown in the genome browser. This will result in a smaller report size. |
| vcf.report.max_records | ||
| vcf.report.max_samples | ||
| vcf.report.template | for details, see here | |
| vcf.report.GRCh38.genes | installed |
Profiles¶
VIP pre-defines two profiles. The default profile is Slurm with fallback to local in case Slurm cannot be discovered.
| key | description |
|---|---|
| local | for details, see here |
| slurm | for details, see here |
Additional profiles (for details, see here) can be added to your configuration file and used on the command-line, for example to run VIP on the Amazon, Azure or Google Cloud.
Process¶
By default, each process gets assigned 4 cpus, 8GB of memory and a max runtime of 4 hours. Depending on your system specifications and your analysis you might need to use updated values. For information on how to update process configuration see the Nextflow documentation.
The following sections list all processes and their non-default configuration.
FASTQ¶
| process label | configuration |
|---|---|
| concat_fastq | default |
| concat_fastq_paired_end | default |
| minimap2_align | cpus=8 memory='16GB' time='23h' |
| minimap2_align_paired_end | cpus=8 memory='16GB' time='23h' |
CRAM¶
| process label | configuration |
|---|---|
| concat_vcf | default |
| cram_validate | default |
| cutesv_call | cpus=4 memory='8GB' time='5h' |
| deepvariant_call | cpus=default memory='2GB * cpus' time='5h' |
| deepvariant_call_duo | cpus=default memory='4GB * cpus' time='5h' |
| deepvariant_call_trio | cpus=default memory='4GB * cpus' time='5h' |
| deepvariant_concat_gvcf | cpus=default memory='2GB' time='30m' |
| deepvariant_concat_vcf | cpus=default memory='2GB' time='30m' |
| deepvariant_joint_call | cpus=default memory='2GB' time='30m' |
| expansionhunter_call | cpus=4 memory='16GB' time='5h' |
| manta_joint_call | cpus=4 memory='8GB' time='5h' |
| straglr_call | default |
| vcf_merge_str | default |
| vcf_merge_sv | default |
gVCF¶
| process label | configuration |
|---|---|
| gvcf_liftover | default |
| gvcf_validate | memory='100MB' time='30m' |
| gvcf_merge | memory='2GB' time='30m' |
VCF¶
| process label | configuration |
|---|---|
| vcf_annotate | cpus=4 memory='8GB' time='4h' |
| vcf_annotate_publish | default |
| vcf_classify | memory = '2GB' |
| vcf_classify_publish | default |
| vcf_classify_samples | memory = '2GB' |
| vcf_classify_samples_publish | default |
| vcf_concat | default |
| vcf_filter | default |
| vcf_filter_samples | default |
| vcf_inheritance | memory = '2GB' |
| vcf_liftover | default |
| vcf_normalize | default |
| vcf_report | memory = '4GB' |
| vcf_slice | default |
| vcf_split | memory='100MB' time='30m' |
| vcf_validate | memory='100MB' time='30m' |
Environment¶
See https://github.com/molgenis/vip/tree/main/config for an overview of available environment variables. Notably this allows to use different Apptainer containers for the tools that VIP relies on.