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:* /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:* /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:* /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:* /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:* /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:* /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:* /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:* /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:* /rules/shared/variant/caller/freebayes.snake - *Rule name:* freebayes__variant_call_mapped_reads **Input(s):**