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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

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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

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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: 2024-04-20

KNIME versions: From v3.6 to v4.7

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