Vardict - Create Wgs Bed File¶
Creates bed file with whole genomic regions in reference fasta file. Simple way to unite WGS and panel analysis.
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/vardict.snake
- Rule name: vardict__create_wgs_bed_file
Input(s):
Vardict - Prepare Bed File¶
Vardict throws error for bed files with more than 4 columns, rule therefore cut other columns
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/vardict.snake
- Rule name: vardict__prepare_bed_file
Input(s):
Vardict - Call Germline Variants¶
Identify small variation (SNP and indels) from the mapped reads.
- Config parameters:
- hard_filter:
- min_nonref_allele_freq min_alternate_count min_map_quality
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/vardict.snake
- Rule name: vardict__call_germline_variants
Input(s):
- bam: Unordered mapped reads in bam format
- bai: Ordered and indexed mapped reads in bam format
- bed: Bed file containing whole genomic regions from the reference fasta
- reffasta: Reference genomic sequences in fasta format
- reffaidx: Indexed reference genomic sequences in fasta.fai format
Output(s):
- vcf: Variants in the Variant Call Format (VCF)
Vardict - Test Strand Bias¶
Perform statistical testing of strand bias.
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/vardict.snake
- Rule name: vardict__test_strand_bias
Input(s):
Vardict - Tsb To Vcf¶
Convert intermediate files of Vardict to VCF format
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/vardict.snake
- Rule name: vardict__tsb_to_vcf
Input(s):
Clair - Variant Call Mapped Reads¶
Identify small variants from reads mapped to a reference.
- Config parameters:
- hard_filter:
- min_nonref_allele_freq min_coverage
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/clair.snake
- Rule name: clair__variant_call_mapped_reads
Input(s):
- bam: Unordered mapped reads in bam format
- bai: Ordered and indexed mapped reads in bam format
- reffasta: Reference genomic sequences in fasta format
- reffaidx: Indexed reference genomic sequences in fasta.fai format
Output(s):
- vcf: Variants in the Variant Call Format (VCF)
Vcfcat - Merge Vcf Files¶
Concatente all vcf files into one
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/clair.snake
- Rule name: vcfcat__merge_vcf_files
Input(s):
Medaka - Variant Call Mapped Reads¶
Identify small variants from reads mapped to a reference. Mainly for diploid samples.
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/medaka.snake
- Rule name: medaka__variant_call_mapped_reads
Input(s):
- bam: Unordered mapped reads in bam format
- reffasta: Reference genomic sequences in fasta format
- reffaidx: Indexed reference genomic sequences in fasta.fai format
Output(s):
- vcf: Variants in the Variant Call Format (VCF)
Freebayes - Variant Call Mapped Reads¶
Identify small variation (SNP and indels) from the mapped reads.
Location
- Filepath: <SnakeLines_dir>/rules/shared/variant/caller/freebayes.snake
- Rule name: freebayes__variant_call_mapped_reads
Input(s):