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test v0.2.6
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@andyjslee
andyjslee committed Jul 15, 2024
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19 changes: 10 additions & 9 deletions README.md
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## 04. Available Commands

| Command | Description |
| ------- |-----------------------------------------------------------------------------------------------------------------------------|
| annotate | Annotate variant calls using [pyensembl](https://github.com/openvax/pyensembl) or [gencode](https://www.gencodegenes.org/). |
| collapse | Collapse a variants list into unique variants. |
| diff | Identify variant calls specific to a list. |
| filter | Filter variant calls (can be used to identify somatic variants). |
| Command | Description |
|-----------|-----------------------------------------------------------------------------------------------------------------------------|
| annotate | Annotate variant calls using [pyensembl](https://github.com/openvax/pyensembl) or [gencode](https://www.gencodegenes.org/). |
| collapse | Collapse a variants list into unique variants. |
| diff | Identify variant calls specific to a list. |
| filter | Filter variant calls (can be used to identify somatic variants). |
| intersect | Identify intersecting variant calls. |
| merge | Merge variant calls from various variant callers. |
| overlap | Identify variants that overlap with a list of genomic ranges. |
| vcf2tsv | Convert a VCF file (see below for supported variant callers) to a TSV file. |
| merge | Merge variant calls from various variant callers. |
| overlap | Identify variants that overlap with a list of genomic ranges. |
| score | Calculates average alignment score for each breakpoint. |
| vcf2tsv | Convert a VCF file (see below for supported variant callers) to a TSV file. |

## 05. Supported Variant Callers

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404 changes: 202 additions & 202 deletions examples/outputs/hg002_deepvariant.tsv
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6 changes: 3 additions & 3 deletions examples/outputs/hg002_hg001_delly2.tsv
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variant_id variant_call_id sample_id chromosome_1 position_1 chromosome_2 position_2 variant_type reference_allele alternate_allele source_id phase_block_id clone_id nucleic_acid variant_calling_method sequencing_platform filter quality_score precise variant_subtype variant_size reference_allele_read_count alternate_allele_read_count total_read_count alternate_allele_fraction alternate_allele_read_ids variant_sequences tags attributes position_1_annotation_annotator position_1_annotation_annotator_version position_1_annotation_gene_id position_1_annotation_gene_id_stable position_1_annotation_gene_name position_1_annotation_gene_strand position_1_annotation_gene_type position_1_annotation_gene_version position_1_annotation_region position_1_annotation_species position_2_annotation_annotator position_2_annotation_annotator_version position_2_annotation_gene_id position_2_annotation_gene_id_stable position_2_annotation_gene_name position_2_annotation_gene_strand position_2_annotation_gene_type position_2_annotation_gene_version position_2_annotation_region position_2_annotation_species
1 hg002_dna_delly2-somatic_1_DUP_chr4:49149266_chr4:49149853 hg002 chr4 49149266 chr4 49149853 DUP A <DUP> hg002 dna delly2-somatic ILMN PASS 413.0 True -1 0 30 30 1.0 ID=DUP00000399;PRECISE=False;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.1.7;END=49149853;PE=10;MAPQ=40;CT=5to3;CIPOS=-50,50;CIEND=-50,50;RDRATIO=2.30714;SOMATIC=True;GT=1/1;GL=-84.8452,-7.97613,0;GQ=80;FT=PASS;RCL=4124;RC=376812;RCR=1538;RDCN=133;DR=0;DV=30;RR=0;RV=0
1 hg001_dna_delly2-somatic_2_DUP_chr4:49149266_chr4:49149853 hg001 chr4 49149266 chr4 49149853 DUP A <DUP> hg002 dna delly2-somatic ILMN PASS 413.0 True -1 2 0 2 0.0 ID=DUP00000399;PRECISE=False;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.1.7;END=49149853;PE=10;MAPQ=40;CT=5to3;CIPOS=-50,50;CIEND=-50,50;RDRATIO=2.30714;SOMATIC=True;GT=0/0;GL=0,-0.596514,-5.89445;GQ=7;FT=LowQual;RCL=8048;RC=287707;RCR=1926;RDCN=58;DR=2;DV=0;RR=0;RV=0
variant_id variant_call_id sample_id chromosome_1 position_1 chromosome_2 position_2 variant_type reference_allele alternate_allele source_id phase_block_id clone_id nucleic_acid variant_calling_method sequencing_platform filter quality_score precise variant_subtype variant_size reference_allele_read_count alternate_allele_read_count total_read_count alternate_allele_fraction alternate_allele_read_ids variant_sequences tags attributes average_alignment_score_window position_1_average_alignment_score position_2_average_alignment_score position_1_annotation_annotator position_1_annotation_annotator_version position_1_annotation_gene_id position_1_annotation_gene_id_stable position_1_annotation_gene_name position_1_annotation_gene_strand position_1_annotation_gene_type position_1_annotation_gene_version position_1_annotation_region position_1_annotation_species position_2_annotation_annotator position_2_annotation_annotator_version position_2_annotation_gene_id position_2_annotation_gene_id_stable position_2_annotation_gene_name position_2_annotation_gene_strand position_2_annotation_gene_type position_2_annotation_gene_version position_2_annotation_region position_2_annotation_species
1 hg002_dna_delly2-somatic_1_DUP_chr4:49149266_chr4:49149853 hg002 chr4 49149266 chr4 49149853 DUP A <DUP> hg002 dna delly2-somatic ILMN PASS 413.0 True -1 0 30 30 1.0 ID=DUP00000399;PRECISE=False;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.1.7;END=49149853;PE=10;MAPQ=40;CT=5to3;CIPOS=-50,50;CIEND=-50,50;RDRATIO=2.30714;SOMATIC=True;GT=1/1;GL=-84.8452,-7.97613,0;GQ=80;FT=PASS;RCL=4124;RC=376812;RCR=1538;RDCN=133;DR=0;DV=30;RR=0;RV=0 -1 -1.0 -1.0
1 hg001_dna_delly2-somatic_2_DUP_chr4:49149266_chr4:49149853 hg001 chr4 49149266 chr4 49149853 DUP A <DUP> hg002 dna delly2-somatic ILMN PASS 413.0 True -1 2 0 2 0.0 ID=DUP00000399;PRECISE=False;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.1.7;END=49149853;PE=10;MAPQ=40;CT=5to3;CIPOS=-50,50;CIEND=-50,50;RDRATIO=2.30714;SOMATIC=True;GT=0/0;GL=0,-0.596514,-5.89445;GQ=7;FT=LowQual;RCL=8048;RC=287707;RCR=1926;RDCN=58;DR=2;DV=0;RR=0;RV=0 -1 -1.0 -1.0
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