This node is currently not available in KNIME v5.4 — instead we’re showing this page for KNIME v4.7. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.

Casbar

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

: 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]
: SAM input file containing four-letter read alignments (must be sorted by coordinates). [bam,sam,sam.bgzf,sam.gz]

Output Ports

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

Popular Predecessors

Bisar100 %

Popular Successors

No recommendations found

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.)

Workflows

BS-Seq Analysis WorkflowSeqAn

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.

Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Plugin version: 2.4.1.202004061533

On NodePit since: 2022-12-06

Last update: 2024-12-23

KNIME versions: From v3.6 to v4.7

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!