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Variant Parameter Cleanup (from PR#110) #136

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Nov 14, 2023
Merged

Variant Parameter Cleanup (from PR#110) #136

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45504d6
make use of var frequency variables more consistent
malachig Apr 11, 2023
d37fa0d
make use of var frequency variables more consistent
malachig Apr 11, 2023
3a18642
fix min var freq variables for tumor only variant calling wdls
malachig Apr 11, 2023
e06cac3
the cutoff used for varscan tool and fp_filter of varscan results sho…
malachig Apr 13, 2023
24aed9b
pass llr settings in from immuno and drop defaults being set everywhere
malachig Apr 13, 2023
7548f31
remove incorrect input
malachig Apr 13, 2023
d312b40
remove incorrect input
malachig Apr 14, 2023
cf974ec
make parameters optional now that defaults are not being specified
malachig Apr 21, 2023
3041349
fix missing default on input
malachig Apr 21, 2023
35df3ed
fix another missing default on inputs
malachig Apr 21, 2023
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24 changes: 14 additions & 10 deletions definitions/detect_variants.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -36,12 +36,14 @@ workflow detectVariants {
Boolean strelka_exome_mode
Int strelka_cpu_reserved = 8

Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.1
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq

Float? fp_min_var_freq

File docm_vcf
File docm_vcf_tbi

Expand All @@ -65,9 +67,9 @@ workflow detectVariants {
Float filter_gnomADe_maximum_population_allele_frequency = 0.001

Float filter_mapq0_threshold = 0.15
Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1
Float filter_somatic_llr_normal_contamination_rate = 0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate
Int filter_minimum_depth = 1
Boolean cle_vcf_filter = false
Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"]
Expand All @@ -89,7 +91,8 @@ workflow detectVariants {
normal_bam=normal_bam,
normal_bam_bai=normal_bam_bai,
interval_list=roi_intervals,
scatter_count=scatter_count
scatter_count=scatter_count,
fp_min_var_freq=fp_min_var_freq
}

call sapp.strelkaAndPostProcessing as strelka {
Expand All @@ -105,7 +108,8 @@ workflow detectVariants {
exome_mode=strelka_exome_mode,
cpu_reserved=strelka_cpu_reserved,
normal_sample_name=normal_sample_name,
tumor_sample_name=tumor_sample_name
tumor_sample_name=tumor_sample_name,
fp_min_var_freq=fp_min_var_freq
}

call vpapp.varscanPreAndPostProcessing as varscan {
Expand All @@ -121,7 +125,7 @@ workflow detectVariants {
scatter_count=scatter_count,
strand_filter=varscan_strand_filter,
min_coverage=varscan_min_coverage,
min_var_freq=varscan_min_var_freq,
varscan_min_var_freq=varscan_min_var_freq,
p_value=varscan_p_value,
max_normal_freq=varscan_max_normal_freq,
normal_sample_name=normal_sample_name,
Expand Down
24 changes: 14 additions & 10 deletions definitions/detect_variants_nonhuman.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -33,12 +33,14 @@ workflow detectVariantsNonhuman {
Boolean strelka_exome_mode
Int strelka_cpu_reserved = 8

Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.1
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq

Float? fp_min_var_freq

File vep_cache_dir_zip
String vep_ensembl_assembly
String vep_ensembl_version
Expand All @@ -53,9 +55,9 @@ workflow detectVariantsNonhuman {
Int? readcount_minimum_mapping_quality

Float filter_mapq0_threshold = 0.15
Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1
Float filter_somatic_llr_normal_contamination_rate = 0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate
Int filter_minimum_depth = 1
Boolean cle_vcf_filter = false
Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"]
Expand All @@ -74,7 +76,8 @@ workflow detectVariantsNonhuman {
normal_bam=normal_bam,
normal_bam_bai=normal_bam_bai,
interval_list=roi_intervals,
scatter_count=scatter_count
scatter_count=scatter_count,
fp_min_var_freq=fp_min_var_freq
}

call sapp.strelkaAndPostProcessing as strelka {
Expand All @@ -90,7 +93,8 @@ workflow detectVariantsNonhuman {
exome_mode=strelka_exome_mode,
cpu_reserved=strelka_cpu_reserved,
normal_sample_name=normal_sample_name,
tumor_sample_name=normal_sample_name
tumor_sample_name=normal_sample_name,
fp_min_var_freq=fp_min_var_freq
}

call vpapp.varscanPreAndPostProcessing as varscan {
Expand All @@ -106,7 +110,7 @@ workflow detectVariantsNonhuman {
scatter_count=scatter_count,
strand_filter=varscan_strand_filter,
min_coverage=varscan_min_coverage,
min_var_freq=varscan_min_var_freq,
varscan_min_var_freq=varscan_min_var_freq,
p_value=varscan_p_value,
max_normal_freq=varscan_max_normal_freq,
normal_sample_name=normal_sample_name,
Expand Down
23 changes: 13 additions & 10 deletions definitions/detect_variants_wgs.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,12 @@ workflow detectVariantsWgs {
Int? readcount_minimum_base_quality
Int? readcount_minimum_mapping_quality
Int scatter_count
Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.1
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq
Float? fp_min_var_freq
File docm_vcf
File docm_vcf_tbi
Boolean filter_docm_variants = true
Expand All @@ -55,9 +56,9 @@ workflow detectVariantsWgs {
Float filter_gnomADe_maximum_population_allele_frequency = 0.001
Float filter_mapq0_threshold = 0.15
Int filter_minimum_depth = 1
Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1
Float filter_somatic_llr_normal_contamination_rate = 0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate
Boolean cle_vcf_filter = false
Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"]
Array[String] variants_to_table_genotype_fields = ["GT", "AD"]
Expand All @@ -80,7 +81,8 @@ workflow detectVariantsWgs {
normal_bam_bai=normal_bam_bai,
interval_list=roi_intervals,
scatter_count=scatter_count,
tumor_sample_name=tumor_sample_name
tumor_sample_name=tumor_sample_name,
fp_min_var_freq=fp_min_var_freq
}

call sapp.strelkaAndPostProcessing as strelka {
Expand All @@ -101,7 +103,8 @@ workflow detectVariantsWgs {
exome_mode=strelka_exome_mode,
cpu_reserved=strelka_cpu_reserved,
call_regions=strelka_call_regions,
call_regions_tbi=strelka_call_regions_tbi
call_regions_tbi=strelka_call_regions_tbi,
fp_min_var_freq=fp_min_var_freq
}

call vpapp.varscanPreAndPostProcessing as varscan {
Expand All @@ -122,7 +125,7 @@ workflow detectVariantsWgs {
scatter_count=scatter_count,
strand_filter=varscan_strand_filter,
min_coverage=varscan_min_coverage,
min_var_freq=varscan_min_var_freq,
varscan_min_var_freq=varscan_min_var_freq,
p_value=varscan_p_value,
max_normal_freq=varscan_max_normal_freq
}
Expand Down
19 changes: 15 additions & 4 deletions definitions/immuno.wdl
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Expand Up @@ -156,12 +156,14 @@ workflow immuno {
Int strelka_cpu_reserved = 8
Int scatter_count = 50

Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.05
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq

Float? fp_min_var_freq

File docm_vcf
File docm_vcf_tbi

Expand All @@ -179,6 +181,11 @@ workflow immuno {
# one of [pick, flag_pick, pick-allele, per_gene, pick_allele_gene, flag_pick_allele, flag_pick_allele_gene]
String? vep_pick
Boolean cle_vcf_filter = false

Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate

Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"]
Array[String] variants_to_table_genotype_fields = ["GT", "AD"]
Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"]
Expand Down Expand Up @@ -332,6 +339,7 @@ workflow immuno {
varscan_min_var_freq=varscan_min_var_freq,
varscan_p_value=varscan_p_value,
varscan_max_normal_freq=varscan_max_normal_freq,
fp_min_var_freq=fp_min_var_freq,
docm_vcf=docm_vcf,
docm_vcf_tbi=docm_vcf_tbi,
filter_docm_variants=filter_docm_variants,
Expand All @@ -343,6 +351,9 @@ workflow immuno {
annotate_coding_only=annotate_coding_only,
vep_pick=vep_pick,
cle_vcf_filter=cle_vcf_filter,
filter_somatic_llr_threshold=filter_somatic_llr_threshold,
filter_somatic_llr_tumor_purity=filter_somatic_llr_tumor_purity,
filter_somatic_llr_normal_contamination_rate=filter_somatic_llr_normal_contamination_rate,
variants_to_table_fields=variants_to_table_fields,
variants_to_table_genotype_fields=variants_to_table_genotype_fields,
vep_to_table_fields=vep_to_table_fields,
Expand Down
17 changes: 10 additions & 7 deletions definitions/somatic_exome.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -56,12 +56,14 @@ workflow somaticExome {
Int strelka_cpu_reserved = 8
Int scatter_count = 50

Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.05
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq

Float? fp_min_var_freq

File docm_vcf
File docm_vcf_tbi

Expand All @@ -70,9 +72,9 @@ workflow somaticExome {
String? gnomad_field_name
Float? filter_gnomADe_maximum_population_allele_frequency

Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1
Float filter_somatic_llr_normal_contamination_rate = 0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate

File vep_cache_dir_zip
String vep_ensembl_assembly
Expand Down Expand Up @@ -208,6 +210,7 @@ workflow somaticExome {
varscan_min_var_freq=varscan_min_var_freq,
varscan_p_value=varscan_p_value,
varscan_max_normal_freq=varscan_max_normal_freq,
fp_min_var_freq=fp_min_var_freq,
docm_vcf=docm_vcf,
docm_vcf_tbi=docm_vcf_tbi,
gnomad_field_name=gnomad_field_name,
Expand Down
16 changes: 9 additions & 7 deletions definitions/somatic_exome_cle.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -46,20 +46,21 @@ workflow somaticExomeCle {
Int qc_minimum_base_quality = 0
Int strelka_cpu_reserved = 8
Int scatter_count
Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.05
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq
Float? fp_min_var_freq
File docm_vcf
File docm_vcf_tbi
String? gnomad_field_name
Float? filter_gnomADe_maximum_population_allele_frequency
Boolean filter_docm_variants = true
Int filter_minimum_depth = 20
Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1.0
Float filter_somatic_llr_normal_contamination_rate = 0.0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate
File vep_cache_dir_zip
String vep_ensembl_assembly
String vep_ensembl_version
Expand Down Expand Up @@ -169,6 +170,7 @@ workflow somaticExomeCle {
varscan_min_var_freq=varscan_min_var_freq,
varscan_p_value=varscan_p_value,
varscan_max_normal_freq=varscan_max_normal_freq,
fp_min_var_freq=fp_min_var_freq,
docm_vcf=docm_vcf,
docm_vcf_tbi=docm_vcf_tbi,
gnomad_field_name=gnomad_field_name,
Expand Down
17 changes: 10 additions & 7 deletions definitions/somatic_exome_nonhuman.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -43,12 +43,14 @@ workflow somaticExomeNonhuman {
Int strelka_cpu_reserved = 8
Int scatter_count = 50

Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.1
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq

Float? fp_min_var_freq

File vep_cache_dir_zip
String vep_ensembl_assembly
String vep_ensembl_version
Expand All @@ -59,9 +61,9 @@ workflow somaticExomeNonhuman {
String? vep_pick
Boolean cle_vcf_filter = false

Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1
Float filter_somatic_llr_normal_contamination_rate = 0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate

Array[String] vep_to_table_fields = ["Consequence", "SYMBOL", "Feature"]
Array[String] variants_to_table_genotype_fields = ["GT", "AD"]
Expand Down Expand Up @@ -142,6 +144,7 @@ workflow somaticExomeNonhuman {
varscan_min_var_freq=varscan_min_var_freq,
varscan_p_value=varscan_p_value,
varscan_max_normal_freq=varscan_max_normal_freq,
fp_min_var_freq=fp_min_var_freq,
filter_somatic_llr_threshold=filter_somatic_llr_threshold,
filter_somatic_llr_tumor_purity=filter_somatic_llr_tumor_purity,
filter_somatic_llr_normal_contamination_rate=filter_somatic_llr_normal_contamination_rate,
Expand Down
17 changes: 9 additions & 8 deletions definitions/somatic_wgs.wdl
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Expand Up @@ -51,19 +51,19 @@ workflow somaticWgs {
File? strelka_call_regions
File? strelka_call_regions_tbi
Int scatter_count
Int varscan_strand_filter = 0
Int varscan_min_coverage = 8
Float varscan_min_var_freq = 0.05
Float varscan_p_value = 0.99
Int? varscan_strand_filter
Int? varscan_min_coverage
Float? varscan_min_var_freq
Float? varscan_p_value
Float? varscan_max_normal_freq
Float? fp_min_var_freq
File docm_vcf
File docm_vcf_tbi
Boolean filter_docm_variants = true


Float filter_somatic_llr_threshold = 5
Float filter_somatic_llr_tumor_purity = 1
Float filter_somatic_llr_normal_contamination_rate = 0
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate
File vep_cache_dir_zip
String vep_ensembl_assembly
String vep_ensembl_version
Expand Down Expand Up @@ -192,6 +192,7 @@ workflow somaticWgs {
varscan_min_var_freq=varscan_min_var_freq,
varscan_p_value=varscan_p_value,
varscan_max_normal_freq=varscan_max_normal_freq,
fp_min_var_freq=fp_min_var_freq,
docm_vcf=docm_vcf,
docm_vcf_tbi=docm_vcf_tbi,
filter_docm_variants=filter_docm_variants,
Expand Down
6 changes: 3 additions & 3 deletions definitions/subworkflows/filter_vcf.wdl
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Expand Up @@ -18,9 +18,9 @@ workflow filterVcf {
File tumor_bam
File tumor_bam_bai
Boolean do_cle_vcf_filter
Float filter_somatic_llr_threshold
Float filter_somatic_llr_tumor_purity
Float filter_somatic_llr_normal_contamination_rate
Float? filter_somatic_llr_threshold
Float? filter_somatic_llr_tumor_purity
Float? filter_somatic_llr_normal_contamination_rate
File reference
File reference_fai
File reference_dict
Expand Down
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