Tools for creating, merging, and filtering aliquot-level GDC MAFs. These tools depend on the
maf-lib library and requires strict schema definitions.
There are three main utilities in the aliquot-maf-tools software:
VcfToAliquotMaf- Converts a single GDC annotated VCF to a caller-specific aliquot MAFMergeAliquotMafs- Takes 2 or more caller-specific aliquot MAFs for a single tumor/normal pair and merges into a merged multi-caller MAFMaskMergedAliquotMaf- Filters the merged multi-caller MAF
All of the implementations use the format:
aliquot-maf-tools VcfToAliquotMaf \
--input_vcf <path to input annotated VCF> \
--output_maf <path to output MAF> \
<schema version> <OPTIONS>
We expect the VCF file to come from the annotation workflow using VEP.
Note: tumor only isn't fully supported yet
usage: GDC Aliquot MAF Tools VcfToAliquotMaf gdc-1.0.0-aliquot
[-h] [--tumor_only] [-t TUMOR_VCF_ID] [-n NORMAL_VCF_ID] --caller_id
CALLER_ID --src_vcf_uuid SRC_VCF_UUID --case_uuid CASE_UUID
--tumor_submitter_id TUMOR_SUBMITTER_ID --tumor_aliquot_uuid
TUMOR_ALIQUOT_UUID --tumor_bam_uuid TUMOR_BAM_UUID
[--normal_submitter_id NORMAL_SUBMITTER_ID]
[--normal_aliquot_uuid NORMAL_ALIQUOT_UUID]
[--normal_bam_uuid NORMAL_BAM_UUID] [--sequencer SEQUENCER]
--maf_center MAF_CENTER --biotype_priority_file BIOTYPE_PRIORITY_FILE
--effect_priority_file EFFECT_PRIORITY_FILE [--custom_enst CUSTOM_ENST]
[--dbsnp_priority_db DBSNP_PRIORITY_DB] --reference_fasta
REFERENCE_FASTA --reference_fasta_index REFERENCE_FASTA_INDEX
[--reference_context_size REFERENCE_CONTEXT_SIZE]
[--cosmic_vcf COSMIC_VCF] [--non_tcga_exac_vcf NON_TCGA_EXAC_VCF]
[--hotspot_tsv HOTSPOT_TSV] [--exac_freq_cutoff EXAC_FREQ_CUTOFF]
[--gdc_blacklist GDC_BLACKLIST] [--min_n_depth MIN_N_DEPTH]
[--gdc_pon_vcf GDC_PON_VCF] [--nonexonic_intervals NONEXONIC_INTERVALS]
[--target_intervals TARGET_INTERVALS]
optional arguments:
-h, --help show this help message and exit
VCF options:
--tumor_only Is this a tumor-only VCF?
-t TUMOR_VCF_ID, --tumor_vcf_id TUMOR_VCF_ID
Name of the tumor sample in the VCF
-n NORMAL_VCF_ID, --normal_vcf_id NORMAL_VCF_ID
Name of the normal sample in the VCF
--caller_id CALLER_ID
Name of the caller used to detect mutations
--src_vcf_uuid SRC_VCF_UUID
The UUID of the src VCF file
Sample Metadata:
--case_uuid CASE_UUID
Sample case UUID
--tumor_submitter_id TUMOR_SUBMITTER_ID
Tumor sample aliquot submitter ID
--tumor_aliquot_uuid TUMOR_ALIQUOT_UUID
Tumor sample aliquot UUID
--tumor_bam_uuid TUMOR_BAM_UUID
Tumor sample bam UUID
--normal_submitter_id NORMAL_SUBMITTER_ID
Normal sample aliquot submitter ID
--normal_aliquot_uuid NORMAL_ALIQUOT_UUID
Normal sample aliquot UUID
--normal_bam_uuid NORMAL_BAM_UUID
Normal sample bam UUID
--sequencer SEQUENCER
The sequencer used
--maf_center MAF_CENTER
The sequencing center
Annotation Resources:
--biotype_priority_file BIOTYPE_PRIORITY_FILE
Biotype priority JSON
--effect_priority_file EFFECT_PRIORITY_FILE
Effect priority JSON
--custom_enst CUSTOM_ENST
Optional custom ENST overrides
--dbsnp_priority_db DBSNP_PRIORITY_DB
DBSNP priority sqlite database
--reference_fasta REFERENCE_FASTA
Reference fasta file
--reference_fasta_index REFERENCE_FASTA_INDEX
Reference fasta fai file
--reference_context_size REFERENCE_CONTEXT_SIZE
Number of BP to add both upstream and downstream from
variant for reference context
--cosmic_vcf COSMIC_VCF
Optional COSMIC VCF for annotating
--non_tcga_exac_vcf NON_TCGA_EXAC_VCF
Optional non-TCGA ExAC VCF for annotating and
filtering
--hotspot_tsv HOTSPOT_TSV
Optional hotspot TSV
Filtering Options:
--exac_freq_cutoff EXAC_FREQ_CUTOFF
Flag variants where the allele frequency in any ExAC
population is great than this value as common_in_exac
[0.001]
--gdc_blacklist GDC_BLACKLIST
The file containing the blacklist tags and tumor
aliquot uuids to apply them to.
--min_n_depth MIN_N_DEPTH
Flag variants where normal depth is <= INT as ndp [7].
--gdc_pon_vcf GDC_PON_VCF
The tabix-indexed panel of normals VCF for applying
the gdc pon filter
--nonexonic_intervals NONEXONIC_INTERVALS
Flag variants outside of this tabix-indexed bed file
as NonExonic
--target_intervals TARGET_INTERVALS
Flag variants outside of these tabix-indexed bed files
as off_target. Use one or more times.
Note: we developed this to work with VEP v102
usage: GDC Aliquot MAF Tools VcfToAliquotMaf gdc-2.0.0-aliquot
[-h] [--tumor_only] [-t TUMOR_VCF_ID] [-n NORMAL_VCF_ID] --caller_id
CALLER_ID --src_vcf_uuid SRC_VCF_UUID --case_uuid CASE_UUID
--tumor_submitter_id TUMOR_SUBMITTER_ID --tumor_aliquot_uuid
TUMOR_ALIQUOT_UUID --tumor_bam_uuid TUMOR_BAM_UUID
[--normal_submitter_id NORMAL_SUBMITTER_ID]
[--normal_aliquot_uuid NORMAL_ALIQUOT_UUID]
[--normal_bam_uuid NORMAL_BAM_UUID] [--sequencer SEQUENCER]
--maf_center MAF_CENTER --biotype_priority_file BIOTYPE_PRIORITY_FILE
--effect_priority_file EFFECT_PRIORITY_FILE [--custom_enst CUSTOM_ENST]
--reference_fasta REFERENCE_FASTA --reference_fasta_index
REFERENCE_FASTA_INDEX [--reference_context_size REFERENCE_CONTEXT_SIZE]
[--cosmic_vcf COSMIC_VCF] [--hotspot_tsv HOTSPOT_TSV]
[--entrez_gene_id_json ENTREZ_GENE_ID_JSON]
[--gnomad_noncancer_vcf GNOMAD_NONCANCER_VCF]
[--gnomad_af_cutoff GNOMAD_AF_CUTOFF] [--gdc_blacklist GDC_BLACKLIST]
[--min_n_depth MIN_N_DEPTH] [--gdc_pon_vcf GDC_PON_VCF]
[--nonexonic_intervals NONEXONIC_INTERVALS]
[--target_intervals TARGET_INTERVALS]
optional arguments:
-h, --help show this help message and exit
VCF options:
--tumor_only Is this a tumor-only VCF?
-t TUMOR_VCF_ID, --tumor_vcf_id TUMOR_VCF_ID
Name of the tumor sample in the VCF
-n NORMAL_VCF_ID, --normal_vcf_id NORMAL_VCF_ID
Name of the normal sample in the VCF
--caller_id CALLER_ID
Name of the caller used to detect mutations
--src_vcf_uuid SRC_VCF_UUID
The UUID of the src VCF file
Sample Metadata:
--case_uuid CASE_UUID
Sample case UUID
--tumor_submitter_id TUMOR_SUBMITTER_ID
Tumor sample aliquot submitter ID
--tumor_aliquot_uuid TUMOR_ALIQUOT_UUID
Tumor sample aliquot UUID
--tumor_bam_uuid TUMOR_BAM_UUID
Tumor sample bam UUID
--normal_submitter_id NORMAL_SUBMITTER_ID
Normal sample aliquot submitter ID
--normal_aliquot_uuid NORMAL_ALIQUOT_UUID
Normal sample aliquot UUID
--normal_bam_uuid NORMAL_BAM_UUID
Normal sample bam UUID
--sequencer SEQUENCER
The sequencer used
--maf_center MAF_CENTER
The sequencing center
Annotation Resources:
--biotype_priority_file BIOTYPE_PRIORITY_FILE
Biotype priority JSON
--effect_priority_file EFFECT_PRIORITY_FILE
Effect priority JSON
--custom_enst CUSTOM_ENST
Optional custom ENST overrides
--reference_fasta REFERENCE_FASTA
Reference fasta file
--reference_fasta_index REFERENCE_FASTA_INDEX
Reference fasta fai file
--reference_context_size REFERENCE_CONTEXT_SIZE
Number of BP to add both upstream and downstream from
variant for reference context
--cosmic_vcf COSMIC_VCF
Optional COSMIC VCF for annotating
--hotspot_tsv HOTSPOT_TSV
Optional hotspot TSV
--entrez_gene_id_json ENTREZ_GENE_ID_JSON
Optional map of ensembl transcript IDs and symbols to
entrez gene ID
--gnomad_noncancer_vcf GNOMAD_NONCANCER_VCF
Path to the bgzipped and tabix-indexed non-cancer
gnomAD allele frequency VCF.
Filtering Options:
--gnomad_af_cutoff GNOMAD_AF_CUTOFF
Flag variants where the allele frequency in any gnomAD
population is greater than this value as
common_in_gnomAD [0.001]
--gdc_blacklist GDC_BLACKLIST
The file containing the blacklist tags and tumor
aliquot uuids to apply them to.
--min_n_depth MIN_N_DEPTH
Flag variants where normal depth is <= INT as ndp [7].
--gdc_pon_vcf GDC_PON_VCF
The tabix-indexed panel of normals VCF for applying
the gdc pon filter
--nonexonic_intervals NONEXONIC_INTERVALS
Flag variants outside of this tabix-indexed bed file
as NonExonic
--target_intervals TARGET_INTERVALS
Flag variants outside of these tabix-indexed bed files
as off_target. Use one or more times.
Merge two or more per-caller aliquot MAFs from the same tumor/normal pair. All implementations use the format:
aliquot-maf-tools MergeAliquotMafs \
--output_maf <path to output merged MAF> \
<schema version> <OPTIONS>
usage: GDC Aliquot MAF Tools MergeAliquotMafs gdc-1.0.0-aliquot-merged
[-h] [--mutect2 MUTECT2] [--muse MUSE] [--vardict VARDICT]
[--varscan2 VARSCAN2] [--somaticsniper SOMATICSNIPER] [--pindel PINDEL]
[--min_n_depth MIN_N_DEPTH]
optional arguments:
-h, --help show this help message and exit
--mutect2 MUTECT2 Path to input protected MuTect2 MAF file
--muse MUSE Path to input protected MuSE MAF file
--vardict VARDICT Path to input protected VarDict MAF file
--varscan2 VARSCAN2 Path to input protected VarScan2 MAF file
--somaticsniper SOMATICSNIPER
Path to input protected SomaticSniper MAF file
--pindel PINDEL Path to input protected Pindel MAF file
--min_n_depth MIN_N_DEPTH
Flag variants where normal depth is <= INT as ndp.
This is performed after averaging depths across
callers [7]
Note: currently only sets RNA columns to unknown/na, annotator not implemented yet
usage: GDC Aliquot MAF Tools MergeAliquotMafs gdc-2.0.0-aliquot-merged
[-h] [--tumor_only] [--mutect2 MUTECT2] [--muse MUSE]
[--vardict VARDICT] [--varscan2 VARSCAN2]
[--somaticsniper SOMATICSNIPER] [--pindel PINDEL]
[--min_n_depth MIN_N_DEPTH]
optional arguments:
-h, --help show this help message and exit
--tumor_only If this is a tumor-only MAF
--mutect2 MUTECT2 Path to input protected MuTect2 MAF file
--muse MUSE Path to input protected MuSE MAF file
--vardict VARDICT Path to input protected VarDict MAF file
--varscan2 VARSCAN2 Path to input protected VarScan2 MAF file
--somaticsniper SOMATICSNIPER
Path to input protected SomaticSniper MAF file
--pindel PINDEL Path to input protected Pindel MAF file
--min_n_depth MIN_N_DEPTH
Flag variants where normal depth is <= INT as ndp.
This is performed after averaging depths across
callers [7]
All of the implementations use the format:
aliquot-maf-tools MaskMergedAliquotMaf \
--input_maff <path to input merged MAF> \
--output_maf <path to output filtered MAF> \
<schema version> <OPTIONS>
usage: GDC Aliquot MAF Tools MaskMergedAliquotMaf gdc-1.0.0-aliquot-merged-masked
[-h] [--tumor_only] [--reference_fasta_index REFERENCE_FASTA_INDEX]
[--min_callers MIN_CALLERS]
optional arguments:
-h, --help show this help message and exit
--tumor_only Is this a tumor-only VCF?
--reference_fasta_index REFERENCE_FASTA_INDEX
Path to the reference fasta fai file if the input MAF
is not sorted
--min_callers MIN_CALLERS
Minimum number of callers required [2]
usage: GDC Aliquot MAF Tools MaskMergedAliquotMaf gdc-2.0.0-aliquot-merged-masked
[-h] [--tumor_only] [--reference_fasta_index REFERENCE_FASTA_INDEX]
[--min_callers MIN_CALLERS]
optional arguments:
-h, --help show this help message and exit
--tumor_only Is this a tumor-only VCF?
--reference_fasta_index REFERENCE_FASTA_INDEX
Path to the reference fasta fai file if the input MAF
is not sorted
--min_callers MIN_CALLERS
Minimum number of callers required [2]