Gatk - Fix Vcf Header¶
Adds missing sequence dictionary to VCF header. This job also generates VCF index (.idx).
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/report/calling/gatk.snake
- Rule name: gatk__fix_vcf_header
Input(s):
- vcf: Raw VCF from variant caller vardict.
- fasta: Reference sequence.
Output(s):
- vcf: Fixed VCF.
- vcf_index: Fixed VCF index.
Tabix - Index Vcf¶
Create tabix intex on BGZF (bgzipped) VCF file.
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/report/calling/gatk.snake
- Rule name: tabix__index_vcf
Input(s):
Picard - Bed To Interval List¶
Conversion of BED file to GATK specific interval_list.
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/report/calling/gatk.snake
- Rule name: picard__bed_to_interval_list
Input(s):
- bed: BED file
- seq_dict: sequence dictionary
Output(s):
- intervals: interval list
Gatk - Collect Variant Calling Metrics¶
GATK tool for generating
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/report/calling/gatk.snake
- Rule name: gatk__collect_variant_calling_metrics
Input(s):
- vcf: called variants
- vcf_index: index of called variants
- dbsnp: DBSNP in BGZF format.
- dbsnp_index: DBSNP index of BGZF format.
- intervals: Genomic regions of interest.
Output(s):
- filename: Text file with summary of calling metrics.