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sv benchmark params are exposed #34

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merged 6 commits into from
May 7, 2024
Merged

sv benchmark params are exposed #34

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5581454
sv benchmark params are exposed
kubranarci Apr 26, 2024
5f3dd65
format lines removed
kubranarci Apr 29, 2024
acfd649
add new params ad meta
kubranarci May 7, 2024
6964ec8
Update assets/schema_input.json
kubranarci May 7, 2024
aca65f4
update utils_nfcore_pipeline
kubranarci May 7, 2024
156eaf7
Update README.md
kubranarci May 7, 2024
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6 changes: 6 additions & 0 deletions README.md
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Expand Up @@ -47,6 +47,12 @@
Supported SV callers: Manta, SVaba, Dragen, Delly, Lumpy ..
Available Truth samples: HG002, SEQC2

- If you have unresolved SVs, it is recommended to use only truvari with --pctsim 0.

- The size filtration parameters provided by truvari and svbenchmark do not apply in the same way. That is why using them are not recommended through the pipeline, but in vcf normalization steps, variants can be filtering safely.

- Please not that it is not possible to use exactly the same parameters for different benchmarking methods.

<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
Explain what rows and columns represent. For instance (please edit as appropriate):

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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -155,7 +155,7 @@ process {
}
withName: "TRUVARI_BENCH" {
ext.prefix = {"${params.sample}"}
ext.args = {"--pctsize 0.5 --pctovl 0.5 --refdist 1000 --pick ac"}
ext.args = {"--pctsize $params.pctsize --pctovl $params.pctovl --pctseq $params.pctseq --refdist $params.refdist --pick $params.pick --chunksize $params.chunksize"}
ext.when = { params.method.split(',').contains('truvari') }
publishDir = [
path: {"${params.outdir}/${meta.id}/truvari_bench"},
Expand All @@ -165,7 +165,7 @@ process {
}
withName: SVANALYZER_SVBENCHMARK {
ext.prefix = {"${params.sample}"}
ext.args = {"-normshift 0.3 –normdist 0.3 –normsizediff 0.3"}
ext.args = {"-normshift $params.normshift –normdist $params.normdist –normsizediff $params.normsizediff -maxdist $params.maxdist"}
ext.when = { params.method.split(',').contains('svanalyzer') }
publishDir = [
path: {"${params.outdir}/${meta.id}/svanalyzer_bench"},
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21 changes: 17 additions & 4 deletions conf/test_hg38.config
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Expand Up @@ -30,13 +30,26 @@ params {

// Processes
analysis = 'germline' //somatic
method = 'truvari,svanalyzer,wittyer' // --not working for now : vcfdist
method = 'truvari,svanalyzer' // --not working for now : vcfdist
similarity = 0 // determines the sequence similarity level in benchmarking.
preprocess = "normalization, deduplication"
min_sv_size = 50
variant_filtering = "include" // null, include, exclude
expression = 'FILTER="PASS"'

//variant_filtering = "include" // null, include, exclude
//expression = 'FILTER="PASS"'

//truvari benchmark parameters
pctsize = 0.3
pctseq = 0 // has to be 0 for unresolved variants to be benchmarked or when --dup-to-ins unsed
pctovl = 0
refdist = 100000
chunksize = 100000
pick = "ac"

//svanalyzer benchmark parameters
normshift = 0.3
normdist = 0.3
normsizediff = 0.3
maxdist = 100000

sample = "HG002" // available samples: SEQC2, HG002
truth_sv = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg38/truth/HG002_GRCh38_difficult_medical_gene_SV_benchmark_v0.01.chr21.vcf.gz"
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13 changes: 13 additions & 0 deletions nextflow.config
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Expand Up @@ -49,6 +49,19 @@ params {
variant_filtering = null // null, include, exclude
expression = null

//truvari benchmark parameters
pctsize = 0.7
pctseq = 0.7 // has to be 0 for unresolved variants to be benchmarked or when --dup-to-ins unsed
pctovl = 0
refdist = 500
chunksize = 500
pick = "single"

//svanalyzer benchmark parameters
normshift = 0.2
normdist = 0.2
normsizediff = 0.2
maxdist = 100000

// References
genome = null
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61 changes: 50 additions & 11 deletions nextflow_schema.json
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Expand Up @@ -94,67 +94,106 @@
},
"analysis": {
"type": "string",
"format": "directory-path",
"description": "",
"fa_icon": "fas fa-folder-open"
},
"preprocess": {
"type": "string",
"format": "directory-path",
"description": "",
"fa_icon": "fas fa-folder-open"
},
"sv_standardization": {
"type": "string",
"format": "directory-path",
"description": "",
"fa_icon": "fas fa-folder-open"
},
"similarity": {
"type": "integer",
"format": "directory-path",
"description": "",
"fa_icon": "fas fa-folder-open"
},
"method": {
"type": "string",
"format": "directory-path",
"description": "",
"fa_icon": "fas fa-folder-open"
},
"min_sv_size": {
"type": "integer",
"format": "directory-path",
"description": "Maximum SV size of variants to benchmark, 0 to disable , Default:50",
"fa_icon": "fas fa-folder-open"
},
"max_sv_size": {
"type": "integer",
"format": "directory-path",
"description": "Maximum SV size of variants to benchmark, -1 to disable , Default:-1",
"fa_icon": "fas fa-folder-open"
},
"min_allele_freq": {
"type": "number",
"format": "directory-path",
"description": "Minimum Alele Frequency of variants to benchmark, Use -1 to disable , Default:-1",
"fa_icon": "fas fa-folder-open"
},
"min_num_reads": {
"type": "integer",
"format": "directory-path",
"description": "Minimum number of read supporting variants to benchmark, Use, -1 to disable , Default:-1",
"fa_icon": "fas fa-folder-open"
},
"pctsize": {
"type": "number",
"description": "TRUVARI PARAMETER. Ratio of min(base_size, comp_size)/max(base_size, comp_size)",
"fa_icon": "fas fa-folder-open"
},
"refdist": {
"type": "integer",
"description": "TRUVARI PARAMETER. Maximum distance comparison calls must be within from base call's start/end",
"fa_icon": "fas fa-folder-open"
},
"chunksize": {
"type": "integer",
"description": "TRUVARI PARAMETER.",
"fa_icon": "fas fa-folder-open"
},
"pctseq": {
"type": "number",
"description": "TRUVARI PARAMETER. Edit distance ratio between the REF/ALT haplotype sequences of base and comparison call.",
"fa_icon": "fas fa-folder-open"
},
"pctovl": {
"type": "number",
"description": "TRUVARI PARAMETER. Ratio of two calls' (overlapping bases)/(longest span).",
"fa_icon": "fas fa-folder-open"
},
"pick": {
"type": "string",
"description": "TRUVARI PARAMETER.How many matches a variant is allowed to participate in is controlled: single,ac,multi",
"fa_icon": "fas fa-folder-open"
},
"normshift": {
"type": "number",
"description": "SVANALYZER PARAMETER. Disallow matches if alignments between alternate alleles have normalized shift greater than normshift (default 0.2) ",
"fa_icon": "fas fa-folder-open"
},
"normdist": {
"type": "number",
"description": "SVANALYZER PARAMETER. Disallow matches if alternate alleles have normalized edit distance greater than normdist (default 0.2)",
"fa_icon": "fas fa-folder-open"
},
"normsizediff": {
"type": "number",
"description": "SVANALYZER PARAMETER. Disallow matches if alternate alleles have normalized size difference greater than normsizediff (default 0.2) ",
"fa_icon": "fas fa-folder-open"
},
"maxdist": {
"type": "integer",
"description": "SVANALYZER PARAMETER. Disallow matches if positions of two variants are more than maxdist bases from each other (default 100,000).",
"fa_icon": "fas fa-folder-open"
},
"variant_filtering": {
"type": "string",
"format": "directory-path",
"description": "Use either exclude or include to enable variant filtering using bcftools expressions, Default:null",
"fa_icon": "fas fa-folder-open"
},
"expression": {
"type": "string",
"format": "directory-path",
"description": "Use bcftools expressions here https://samtools.github.io/bcftools/bcftools.html#expressions. This must be coupled with variant_expression, Default:null",
"fa_icon": "fas fa-folder-open"
},
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