| 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] |
| snv.whatshap.output_read_list |
|
Write reads that have been used for phasing to FILE. |
| snv.whatshap.algorithm |
whatshap |
Phasing algorithm to use allowed values: [whatshap,hapchat,heuristic] |
| snv.whatshap.merge_reads |
Merge reads which are likely to come from the same haplotype |
|
| snv.whatshap.row_limit |
256 |
For the heuristic: Specifies the maximum number of memorized intermediate solutions. Larger values increase runtime and memory consumption, but can improve phasing quality. |
| snv.whatshap.internal_downsampling |
15 |
Coverage reduction parameter in the internal core phasing algorithm. Higher values increase runtime exponentially while possibly improving phasing quality marginally. Avoid using this in the normal case! |
| snv.whatshap.mapping_quality |
20 |
Minimum mapping quality |
| snv.whatshap.only_snvs |
|
Phase only SNVs |
| snv.whatshap.ignore_read_groups |
|
Ignore read groups in BAM/CRAM header and assume all reads come from the same sample. |
| snv.whatshap.error_rate |
0.15 |
The probability that a nucleotide is wrong in read merging model. |
| snv.whatshap.maximum_error_rate |
0.25 |
The maximum error rate of any edge of the read merging graph before discarding it. |
| snv.whatshap.threshold |
1000000 |
The threshold of the ratio between the probabilities that a pair of reads come from the same haplotype and different haplotypes in the read merging model. |
| snv.whatshap.negative_threshold |
1000 |
The threshold of the ratio between the probabilities that a pair of reads come from different haplotypes and the same haplotype in the read merging model. |
| snv.whatshap.distrust_genotypes |
|
Allow switching variants from hetero- to homozygous in an optimal solution (see documentation). |
| snv.whatshap.include_homozygous |
|
Also work on homozygous variants, which might be turned to heterozygous |
| snv.whatshap.default_gq |
30 |
Default genotype quality used as cost of changing a genotype when no genotype likelihoods are available |
| snv.whatshap.gl_regularizer |
None |
Constant (float) to be used to regularize genotype likelihoods read from input VCF. |
| snv.whatshap.changed_genotype_list |
|
Write list of changed genotypes to FILE. |
| snv.whatshap.recombination_list |
|
Write putative recombination events to FILE. |
| snv.whatshap.recombrate |
1.26 |
Recombination rate in cM/Mb (used with --ped). If given, a constant recombination rate is assumed. |
| snv.whatshap.genmap |
|
File with genetic map (used with --ped) to be used instead of constant recombination rate, i.e. overrides option --recombrate. |
| snv.whatshap.no_genetic_haplotyping |
|
Do not merge blocks that are not connected by reads (i.e. solely based on genotype status). Default: when in --ped mode, merge all blocks that contain at least one homozygous genotype in at least one individual into one block. |
| snv.whatshap.use_ped_samples |
|
Only work on samples mentioned in the provided PED file. |
| snv.whatshap.use_supplementary |
|
Use also supplementary alignments (default: ignore supplementary_ alignments) |
| snv.whatshap.supplementary_distance |
100000 |
Skip supplementary alignments further than DIST bp away from the primary alignment |
| 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 |
2 |
Minimum number of reads that support a SV to be reported. Please note that the default is lower than the default of cuteSV itself to prevent missed SV calls. |
| 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 for translocation |
| sv.cutesv.nanopore.diff_ratio_merging_DEL |
0.3 |
Do not merge breakpoints with basepair identity more than for deletion |
| sv.cutesv.nanopore.diff_ratio_merging_INS |
0.3 |
Do not merge breakpoints with basepair identity more than for insertion |
| 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 for translocation |
| sv.cutesv.pacbio_hifi.diff_ratio_merging_DEL |
0.5 |
Do not merge breakpoints with basepair identity more than for deletion |
| sv.cutesv.pacbio_hifi.diff_ratio_merging_INS |
0.9 |
Do not merge breakpoints with basepair identity more than for insertion |
| 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 |