0 ×

Casbar

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

SNP and methylation level calling in mapped bisulfite read data.

Web Documentation for Casbar

Options

version-check
Turn this option off to disable version update notifications of the application.
multi
Keep non-unique reads.
max-pile
Maximal number of matches allowed to pile up at the same genome position.
merged-max-pile
Do pile up correction on merged lanes.
min-coverage
Minimal required number of reads covering a candidate position.
exclude-border
Exclude read positions within eb base pairs of read borders for SNP calling.
suboptimal
Keep suboptimal reads.
parse-window-size
Genomic window size for parsing reads (concerns memory consumption, choose smaller windows for higher coverage).
intervals
Genomic intervals to analyze. E.g. 21:1000-2000.
bs-conv-rate
Bisulfite conversion rate.
min-mutations
Minimal number of deviating bases for calling.
min-quality
Minimal average quality for calling.
min-map-quality
Minimum base call quality for a match to be considered.
prob-hetero-snp
Heterozygous SNP probability to compute genotype prior probabilities.
prob-homo-snp
Homozygous SNP probability to compute genotype prior probabilities.
min-score
Minimum score to call.
min-prob
Minimum genotype probability to call.
ns-errors-calling
Use empirical error frequencies of Illumina sequencing data to compute likelihoods in bayesian model (corresponding to Dohm et al. 2008).
verbose
Enable verbose output.
very-verbose
Enable very verbose output.
quiet
Set verbosity to a minimum.

Input Ports

Icon
A reference genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
Icon
SAM input file containing four-letter read alignments (must be sorted by coordinates). [bam,sam,sam.bgzf,sam.gz]

Output Ports

Icon
Output file for SNPs. [vcf,vcf.bgzf,vcf.gz]
Icon
Bed output file for methylation level calls. [bed,bed.bgzf,bed.gz]

Views

Casbar Std Output
The text sent to standard out during the execution of Casbar.
Casbar Error Output
The text sent to standard error during the execution of Casbar. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Workflows

Installation

To use this node in KNIME, install SeqAn from the following update site:

KNIME 4.2
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.