Up: Component summary
Up: Component summary
Component
MethylExtractExtracts methylation from a bam file simultaneously with variant calling. The component is a wrapper of the tool MethylExtract
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | DNA Methylation |
| Authors | Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | MethylExtract |
| Source files | component.xml methylExtract.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| bam | BAM | Mandatory | Aligned Bisulfite sequencing bam file |
| refGenome | BinaryFolder | Mandatory | Reference genome used for alignment |
Outputs| Name | Type | Description |
|---|---|---|
| CpGmeth | CSV | Extracted methylation in CpG context. |
| CHGmeth | CSV | Extracted methylation in CHG context. |
| CHHmeth | CSV | Extracted methylation in CHH context. |
| SNVs | VCF | Single nucleotide variations detected in VCF format. |
| analysis | BinaryFolder | Folder containing all produced files other than outputs including logs. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| context | string | "CG" | Contexts to be extracted. Options are "CG", "CHG", "CHH" or "ALL". |
| conversionFiltering | float | 0.9 | The value can be the fraction of methylated non-CpG contexts within a read ( value between 0 and 1) or the absolute number of methylated non-CpG contexts (integers higher than 1). Default value is 0.9, i.e. a read is discarded when more than 90% of its non-CpG contexts are methylated. A value of 0 will turn off the bisulfite check |
| destrand | boolean | false | Merge methylation calls from the two strands in CpG context. |
| firstIgnor | int | 1 | The number of bases to be ignored from the beginning of the reads (both read and mate) |
| lastIgnore | int | 0 | The number of bases to be ignored from the end of the reads (both read and mate). |
| minCoverage | int | 1 | Minimum coverage for a methylation call. |
| paired | boolean | true | Set true for paired-end reads. |
| phredScore | string | "phred33-quals" | Available options: "phred33-quals", "phred64-quals", "solexa-quals" or "solexa1.3-quals". |
| removeChr | boolean | true | Remove chromosomes other than autosomal, sex and mitochondrial chromosomes. |
| removeOverlap | boolean | true | If the read and mate overlaps, consider methylation only one time from the read and ignoring the mate. |
| threads | int | 1 | The number of threads to be used. |
Test cases| Test case | Parameters▼ | IN bam |
IN refGenome |
OUT CpGmeth |
OUT CHGmeth |
OUT CHHmeth |
OUT SNVs |
OUT analysis |
|---|---|---|---|---|---|---|---|---|
| case1 | properties | bam | refGenome | (missing) | (missing) | (missing) | (missing) | (missing) |
|
paired=false, |
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| case2 | properties | bam | refGenome | (missing) | (missing) | (missing) | (missing) | (missing) |
|
context=ALL, |
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