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SnpStore

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

SNP and Indel Calling in Mapped Read Data.

Web Documentation for SnpStore

Options

version-check
Turn this option off to disable version update notifications of the application.
only-successful-candidates
Output only successfully called SNP candidates. Default: Output all candidates.
dont-clip
Ignore clip tags in gff. Default: off.
multi
Keep non-unique fragmentStore.alignedReadStore. Default: off.
hide-qualities
Only show coverage (no qualities) in SNP output file. Default: off.
solexa-qual-offset
Base qualities are encoded as char value - 64 (instead of char - 33).
method
Set method used for SNP calling either threshold based or Maq method.
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. Default: off.
min-coverage
Minimal required number of reads covering a candidate position.
force-call
Always call base if count is >= fc, ignore other parameters. Default: off.
orientation-aware
Distinguish between forward and reverse reads. Default: off.
max-polymer-run
Discard indels in homopolymer runs longer than mpr.
diff-pos
Minimal number of different read positions supporting the mutation.
exclude-border
Exclude read positions within eb base pairs of read borders for SNV calling. Default: off.
suboptimal
Keep suboptimal reads. Default: off
realign
Realign reads around indel candidates. Default: off
parse-window-size
Genomic window size for parsing reads (concerns memory consumption, choose smaller windows for higher coverage).
min-mutations
Minimal number of observed mutations for mutation to be called.
perc-threshold
Minimal percentage of mutational base for mutation to be called.
min-quality
Minimal average quality of mutational base for mutation to be called.
theta
Dependency coefficient.
hetero-rate
Heterozygote rate.
min-map-quality
Minimum base call (mapping) quality for a match to be considered.
corrected-het
Use amplification bias corrected distribution for heterozygotes. Default: off.
mean-alleleFreq
Mean ref allele frequency in heterozygotes.
amp-cycles
Number of amplification cycles.
amp-efficiency
Polymerase efficiency, probability of amplification.
initial-N
Initial allele population size.
min-explained-column
Minimum fraction of alignment column reads explained by genotype call.
indel-threshold
Minimal number of indel-supporting reads required for indel calling.
indel-perc-threshold
Minimal ratio of indel-supporting/covering reads for indel to be called.
indel-quality-thresh
Minimal average quality of inserted base/deletion-neighboring bases for indel to be called.
both-strands-indel
Both strands need to be observed for indel to be called. Default: off.
exclude-border-indel
Same as option -eb but for indel candidates.
log-file
Write log to FILE.
verbose
Enable verbose output.
very-verbose
Enable very verbose output.
quiet
Set verbosity to a minimum.

Input Ports

A reference genome file. [fa,fasta]
Read alignment file(s) sorted by genomic position. [bam,sam,sam.bgzf,sam.gz,gff]

Output Ports

SNP output file (mandatory). [vcf]
Output file for called indels in gff format. Default: off. [gff,Inactive]

Views

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

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