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125 fix germline variant calling #128

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merged 7 commits into from
Sep 25, 2023
Merged

125 fix germline variant calling #128

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6a53056
variable renamed and passed up to immuno
Jul 20, 2023
82dab69
ignore vscode temp files
evelyn-schmidt Jul 24, 2023
db2e609
removing 0.05 from germline_detect_variants, maybe germline_filter sh…
Jul 26, 2023
bbea07a
setting the germline filter value at the top immuno level
Aug 2, 2023
2f2f5e6
setting the value to 1.1
Aug 7, 2023
473e613
change immuno mode
evelyn-schmidt Aug 23, 2023
1881d10
fix mode change germline_detect_variants.wdl
evelyn-schmidt Aug 24, 2023
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
*~
*#*
zips/*
._*
4 changes: 3 additions & 1 deletion definitions/germline_exome.wdl
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Expand Up @@ -48,6 +48,7 @@ workflow germlineExome {
Array[String]? variants_to_table_fields
Array[String]? variants_to_table_genotype_fields
Array[String]? vep_to_table_fields
Float germline_filter_gnomAD_maximum_population_allele_frequency
}

call ae.alignmentExome as alignmentAndQc {
Expand Down Expand Up @@ -105,7 +106,8 @@ workflow germlineExome {
vep_to_table_fields=vep_to_table_fields,
vep_custom_annotations=vep_custom_annotations,
variants_to_table_fields=variants_to_table_fields,
variants_to_table_genotype_fields=variants_to_table_genotype_fields
variants_to_table_genotype_fields=variants_to_table_genotype_fields,
germline_filter_gnomAD_maximum_population_allele_frequency=germline_filter_gnomAD_maximum_population_allele_frequency
}

call btc.bamToCram {
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4 changes: 3 additions & 1 deletion definitions/germline_exome_hla_typing.wdl
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Expand Up @@ -41,6 +41,7 @@ workflow germlineExomeHlaTyping {
Int? qc_minimum_base_quality
Array[VepCustomAnnotation] vep_custom_annotations
String? optitype_name
Float germline_filter_gnomAD_maximum_population_allele_frequency
}

call ge.germlineExome {
Expand Down Expand Up @@ -77,7 +78,8 @@ workflow germlineExomeHlaTyping {
annotate_coding_only=annotate_coding_only,
vep_custom_annotations=vep_custom_annotations,
qc_minimum_mapping_quality=qc_minimum_mapping_quality,
qc_minimum_base_quality=qc_minimum_base_quality
qc_minimum_base_quality=qc_minimum_base_quality,
germline_filter_gnomAD_maximum_population_allele_frequency=germline_filter_gnomAD_maximum_population_allele_frequency
}

call od.optitypeDna as optitype {
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4 changes: 3 additions & 1 deletion definitions/immuno.wdl
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Expand Up @@ -199,6 +199,7 @@ workflow immuno {
Array[Array[String]] gatk_haplotypecaller_intervals
Int? ploidy
String? optitype_name
Float germline_filter_gnomAD_maximum_population_allele_frequency
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Should immuno go ahead and set a default at the top level of 1.0 so that no variants get filtered?

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Testing now! I left germline_filter_gnomAD_maximum_population_allele_frequency set to 0.05 in germline_detect_variants. Would it be more correct style wise to set that value at the top level and have it be passed down?

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I think our general style is to define the defaults as low down as possible (at the tool level), and then pass parameters upward as needed so that they can be overridden (with the override being set as high up as possible, so we don't have to go digging through 8 layers to find it). In the top-level immuno wdl, I think it would be reasonable to set that value such that it always passes all germline variants, since various steps in that workflow depend on it.


# --------- Phase VCF Inputs ---------------------------------------

Expand Down Expand Up @@ -393,7 +394,8 @@ workflow immuno {
annotate_coding_only=annotate_coding_only,
qc_minimum_mapping_quality=qc_minimum_mapping_quality,
qc_minimum_base_quality=qc_minimum_base_quality,
optitype_name="optitype_normal"
optitype_name="optitype_normal",
germline_filter_gnomAD_maximum_population_allele_frequency=germline_filter_gnomAD_maximum_population_allele_frequency
}

call od.optitypeDna as optitype {
Expand Down
4 changes: 2 additions & 2 deletions definitions/subworkflows/germline_detect_variants.wdl
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Expand Up @@ -37,7 +37,7 @@ workflow germlineDetectVariants {
Array[String]? vep_to_table_fields
String final_tsv_prefix = "variants"
String gnomad_field_name = "gnomADe_AF" # only change with gnomad_filter annotation
Float filter_gnomAD_maximum_population_allele_frequency = 0.05
Float germline_filter_gnomAD_maximum_population_allele_frequency = 0.05
}

call f.freemix {
Expand Down Expand Up @@ -87,7 +87,7 @@ workflow germlineDetectVariants {
reference_fai=reference_fai,
reference_dict=reference_dict,
gnomad_field_name=gnomad_field_name,
filter_gnomAD_maximum_population_allele_frequency=filter_gnomAD_maximum_population_allele_frequency,
germline_filter_gnomAD_maximum_population_allele_frequency=germline_filter_gnomAD_maximum_population_allele_frequency,
limit_variant_intervals=limit_variant_intervals
}

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4 changes: 2 additions & 2 deletions definitions/subworkflows/germline_filter_vcf.wdl
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Expand Up @@ -10,7 +10,7 @@ import "../tools/select_variants.wdl" as sv
workflow germlineFilterVcf {
input {
File annotated_vcf
Float filter_gnomAD_maximum_population_allele_frequency
Float germline_filter_gnomAD_maximum_population_allele_frequency
String gnomad_field_name
File limit_variant_intervals
File reference
Expand All @@ -25,7 +25,7 @@ workflow germlineFilterVcf {
call fvcaf.filterVcfCustomAlleleFreq as gnomadFrequencyFilter {
input:
vcf=codingVariantFilter.filtered_vcf,
maximum_population_allele_frequency=filter_gnomAD_maximum_population_allele_frequency,
maximum_population_allele_frequency=germline_filter_gnomAD_maximum_population_allele_frequency,
field_name=gnomad_field_name
}

Expand Down
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