--create-report <Boolean> |
Create a report of information from the variant calling process (default: true) |
--create-table <Boolean> |
Create table with annotated variants (default: false) |
--create-track <Boolean> |
Create a track of variants, useful for further analysis (default: true) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--direction-frequency |
|
Double: 0.0 <= x <= 50.0 |
Variants that are present in less than this percentage of reads in either direction will be removed. (default: 5.0) |
--fixed-variant-probability |
|
Double: 0.0 <= x <= 100.0 |
The required minimum probability that the variant is different from the reference sequence. Lowering this number will increase the number of variants called. (default: 90.0) |
-i, --input <ClcObjectUrl> |
Input data on server |
--ignore-broken-pairs <Boolean> |
When ticked, broken pair reads will be ignored. (default: true) |
--ignore-nonspecific-matches <[READ, REGION, NONE]> |
When ticked, reads that match in several places will be ignored. (default: READ) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--masking-track <ClcObjectUrl> |
Variant detection will only be performed in the specified regions. |
--max-coverage |
|
Integer: >= 1 |
Variants covered by more than this number of reads will not be called. (default: 100000) |
--min-central-quality |
|
Byte: 0 <= x <= 64 |
Minimum quality score for central nucleotide (default: 20) |
--min-count |
|
Integer: >= 1 |
Variants observed in less than this number of reads will not be called. (default: 2) |
--min-coverage |
|
Integer: >= 1 |
Variants covered by less than this number of reads will not be called. (default: 10) |
--min-frequency |
|
Double: 0.0 <= x <= 100.0 |
Variants observed at less than this frequency will not be called. (default: 20.0) |
--min-ignore-read-length |
|
Integer: >= 1 |
When ignoring regions with non-specific matches, this is the minimum read length needed to ignore the region. (default: 20) |
--min-neighborhood-quality |
|
Byte: 0 <= x <= 64 |
Minimum average quality score for the region around the central nucleotide (default: 15) |
--neighborhood-radius |
|
Integer: >= 1 |
Region size for quality filter defined as the distance to both sides of the central nucleotide (default: 5) |
--probabilistic-ploidy |
|
Integer: 1 <= x <= 4 |
The maximum number of different alleles expected. (default: 2) |
--pyro-filter-length <Integer> |
Only variants in homopolymer regions of minimum this length will be removed. (default: 3) |
--pyro-filter-maximum-frequency <Double> |
Only variants with frequency (among reference and homopolymeric reads only) below this value will be removed. (default: 0.8) |
--read-position-significance |
|
Double: 0.0 < x < 100.0 |
Variants that have a read position distribution that is statistically significantly different from the expected with a test at this level will be removed. (default: 1.0) |
--relative-read-direction-significance |
|
Double: 0.0 < x < 100.0 |
Variants that have a read direction distribution that is statistically significantly different from the expected with a test at this level will be removed. (default: 1.0) |
--use-direction-filter <Boolean> |
When ticked, variants that do not meet the read direction requirements specified below will be removed. (default: false) |
--use-pyro-filter <Boolean> |
When ticked, variants that fulfill the pyro-error requirements specified below will be removed. (default: false) |
--use-quality-filter <Boolean> |
When ticked, reads with bases that do not meet the quality requirements specified below will be ignored. (default: false) |
--use-read-position-filter <Boolean> |
When ticked, variants that do not meet the read position requirements specified below will be removed. (default: false) |
--use-relative-read-direction-filter <Boolean> |
When ticked, variants that do not meet the read direction requirements specified below will be removed. (default: true) |
