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/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/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.
Location
- Filepath: <SnakeLines_dir>/rules/variant/caller/vardict.snake
- Rule name: vardict__call_germline_variants
Input(s):
Vardict - Test Strand Bias¶
Perform statistical testing of strand bias.
Location
- Filepath: <SnakeLines_dir>/rules/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/variant/caller/vardict.snake
- Rule name: vardict__tsb_to_vcf
Input(s):