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MethylExtract

Extracts methylation from a bam file simultaneously with variant calling. The component is a wrapper of the tool MethylExtract

Version 1.0
Bundle sequencing
Categories Analysis
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,
removeChr=false,
conversionFiltering=0

case2 properties bam refGenome (missing) (missing) (missing) (missing) (missing)

context=ALL,
destrand=true,
removeChr=false


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