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.

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.)

Workflows

• Variant_Calling_SnpStore_Workflow2SeqAn

Links

• No links available

Developers