--confirm-methylation-contexts-in-reads <Boolean> |
Confirms methylation-contexts in reads to avoid false positive detection in presence of variants. (default: false) |
--control-samples <ClcObjectUrl> |
Control samples Reads Tracks. |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
-i, --input <ClcObjectUrl> |
Input data on server |
--ignore-broken-pairs <Boolean> |
Paired reads mapped as as broken pairs will be ignored. (default: true) |
--ignore-duplicate-matches <Boolean> |
Multiple reads with identical mapping coordinates will be counted once only. (default: true) |
--ignore-non-specific-matches <Boolean> |
Reads/matches mapped ambiguously will be ignored. (default: true) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--max-mean-site-coverage |
|
Double: 0.0 <= x < 1.7976931348623157E308 |
Exclude sample from current window, if it has a higher mean site (cytosine) coverage. (default: 0.0) |
--max-pvalue |
|
Double: 0.0 <= x <= 1.0 |
Suppress output of windows with a higher p-value (i.e. low-signifance windows). (default: 0.05) |
--methylation-context-group <[STANDARD_LITE, STANDARD_FULL, NOME_LITE, NOME_FULL, EXHAUSTIVE]> |
Methylation context group (default: STANDARD_LITE) |
--min-high-confidence-site-count |
|
Integer: 1 <= x <= 2147483647 |
Exclude sample from current window, if it has fewer high-confidence methylation-sites (cytosines). (default: 1) |
--min-high-confidence-site-coverage |
|
Integer: 1 <= x <= 2147483647 |
A site (cytosine) with at least this coverage is considered a high confidence site. (default: 1) |
--min-sample-count |
|
Integer: 1 <= x <= 2147483647 |
Skip window, if fewer case-samples and fewer control-samples. (default: 1) |
--minimum-strand-coverage |
|
Integer: 1 <= x <= 2147483647 |
Supress methylation call, when strand specific coverage too low. (default: 1) |
--output-methylation-levels <Boolean> |
Output track of methylated cytosines. One track for each sample (cases and controls) will be created. (default: true) |
--output-reports <Boolean> |
Create reports from methylation calling (default: false) |
--read1-soft-clip |
|
Integer: 0 <= x <= 10 |
Number of 5'-nucleotides of each Read 1 (and single-end reads) to disregard during methylation calling. (default: 0) |
--read2-soft-clip |
|
Integer: 0 <= x <= 10 |
Number of 5'-nucleotides of each Read 2 to disregard during methylation calling. (default: 0) |
--statistic-mode <[FISHER_EXACT, CHI_SQUARED, ANOVA, NO_TEST]> |
Statistic mode (default: CHI_SQUARED) |
--window-length |
|
Integer: 10 <= x <= 10000 |
When no window track was choosen in the previous step for focusing the analysis, examine differential methylation in windows of this fixed size. (default: 1000) |
--window-track <ClcObjectUrl> |
Only call differential methylation in regions defined by this feature track |
