dindel(1)

[Required] :

--ref arg: fasta reference sequence (should be indexed with .fai file)

--outputFile arg: file-prefix for output results

[Required] Program option:

--analysis arg (=indels) Analysis type:: getCIGARindels: Extract indels from CIGARs of mapped reads, and infer library insert size distributions indels: infer indels realignCandidates: Realign/reposition candidates in candidate file

[Required] BAM input. Choose one of the following:

--bamFile arg: read alignment file (should be indexed)

--bamFiles arg: file containing filepaths for BAMs to be jointly analysed (not possible for --analysis==indels

[Required for analysis == getCIGARindels]: Region to be considered for extraction of candidate indels.:

--region arg: region to be analysed in format start-end, eg. 1000-2000

--tid arg: target sequence (eg 'X')

[Required for analysis == indels]:

--varFile arg: file with candidate variants to be tested.

--varFileIsOneBased: coordinates in varFile are one-based

Output options:

--outputRealignedBAM: output BAM file with realigned reads

--processRealignedBAM arg ABSOLUTE path to script to process realigned BAM: file

--quiet: quiet output

parameters for analysis==indels option:

--doDiploid: analyze data assuming a diploid sequence

--doPooled: estimate haplotype frequencies using Bayesian EM algorithm. May be applied to single individual and pools.

General algorithm parameters:

--faster: use faster but less accurate ungapped read-haplotype alignment model

--filterHaplotypes: prefilter haplotypes based on coverage

`--flankRefSeq arg (=2)`	#bases of reference sequence of indel region
`--flankMaxMismatch arg (=2)`	max number of mismatches in indel region
`--priorSNP arg (=0.001)`	prior probability of a SNP site
`--priorIndel arg (=0.0001)`	prior probability of a detected indel not being a sequencing error
`--width arg (=60)`	number of bases to left and right of indel
`--maxHap arg (=8)`	maximum number of haplotypes in likelihood computation
`--maxRead arg (=10000)`	maximum number of reads in likelihood computation
`--mapQualThreshold arg (=0.98999999999999999)`	lower limit for read mapping quality
`--capMapQualThreshold arg (=100)`	upper limit for read mapping quality in observationmodel_old (phred units)
`--capMapQualFast arg (=45)`	cap mapping quality in alignment using fast ungapped method
	(WARNING: setting it too high (>50)
	might result in significant overcalling!)
`--skipMaxHap arg (=200)`	skip computation if number of haplotypes exceeds this number
`--minReadOverlap arg (=20)`	minimum overlap between read and haplotype
`--maxReadLength arg (=500)`	maximum length of reads
`--minCount arg (=1)`	minimum number of WS observations of indel
`--maxHapReadProd arg (=10000000)`	skip if product of number of reads and haplotypes exceeds this value

--changeINStoN: change sequence of inserted sequence to 'N', so that no penalty is incurred if a read mismatches the inserted sequence

parameters for --pooled option:

`--bayesa0 arg (=0.001)`	Dirichlet a0 parameter haplotype frequency prior
`--bayesType arg (=singlevariant) Bayesian EM program type (all or`	singlevariant or priorpersite)

General algorithm filtering options:

--checkAllCIGARs arg (=1) include all indels at the position of the call site

--filterReadAux arg: match string for exclusion of reads based on auxilary information

Observation model parameters:

`--pError arg (=0.00050000000000000001)`	probability of a read indel
`--pMut arg (=1.0000000000000001e-05)`	probability of a mutation in the read
`--maxLengthIndel arg (=5)`	maximum length of a _sequencing error_ indel in read [not for `--faster` option]

Library options:

--libFile arg: file with library insert histograms (as generated by --analysis getCIGARindels)

Misc results analysis options:

--compareReadHap: compare likelihood differences in reads against haplotypes

--compareReadHapThreshold arg (=0.5) difference threshold for viewing

--showEmpirical: show empirical distribution over nucleotides

--showCandHap: show candidate haplotypes for fast method

--showHapAlignments: show for each haplotype which reads map to it

--showReads: show reads

--inferenceMethod arg (=empirical): inference method

--opl: output likelihoods for every read and haplotype

[Required] :

--ref arg: fasta reference sequence (should be indexed with .fai file)

--outputFile arg: file-prefix for output results

[Required] Program option:

--analysis arg (=indels) Analysis type:: getCIGARindels: Extract indels from CIGARs of mapped reads, and infer library insert size distributions indels: infer indels realignCandidates: Realign/reposition candidates in candidate file

[Required] BAM input. Choose one of the following:

--bamFile arg: read alignment file (should be indexed)

--bamFiles arg: file containing filepaths for BAMs to be jointly analysed (not possible for --analysis==indels

[Required for analysis == getCIGARindels]: Region to be considered for extraction of candidate indels.:

--region arg: region to be analysed in format start-end, eg. 1000-2000

--tid arg: target sequence (eg 'X')

[Required for analysis == indels]:

--varFile arg: file with candidate variants to be tested.

--varFileIsOneBased: coordinates in varFile are one-based

Output options:

--outputRealignedBAM: output BAM file with realigned reads

--processRealignedBAM arg ABSOLUTE path to script to process realigned BAM: file

--quiet: quiet output

parameters for analysis==indels option:

--doDiploid: analyze data assuming a diploid sequence

--doPooled: estimate haplotype frequencies using Bayesian EM algorithm. May be applied to single individual and pools.

General algorithm parameters:

--faster: use faster but less accurate ungapped read-haplotype alignment model

--filterHaplotypes: prefilter haplotypes based on coverage

`--flankRefSeq arg (=2)`	#bases of reference sequence of indel region
`--flankMaxMismatch arg (=2)`	max number of mismatches in indel region
`--priorSNP arg (=0.001)`	prior probability of a SNP site
`--priorIndel arg (=0.0001)`	prior probability of a detected indel not being a sequencing error
`--width arg (=60)`	number of bases to left and right of indel
`--maxHap arg (=8)`	maximum number of haplotypes in likelihood computation
`--maxRead arg (=10000)`	maximum number of reads in likelihood computation
`--mapQualThreshold arg (=0.98999999999999999)`	lower limit for read mapping quality
`--capMapQualThreshold arg (=100)`	upper limit for read mapping quality in observationmodel_old (phred units)
`--capMapQualFast arg (=45)`	cap mapping quality in alignment using fast ungapped method
	(WARNING: setting it too high (>50)
	might result in significant overcalling!)
`--skipMaxHap arg (=200)`	skip computation if number of haplotypes exceeds this number
`--minReadOverlap arg (=20)`	minimum overlap between read and haplotype
`--maxReadLength arg (=500)`	maximum length of reads
`--minCount arg (=1)`	minimum number of WS observations of indel
`--maxHapReadProd arg (=10000000)`	skip if product of number of reads and haplotypes exceeds this value

--changeINStoN: change sequence of inserted sequence to 'N', so that no penalty is incurred if a read mismatches the inserted sequence

parameters for --pooled option:

`--bayesa0 arg (=0.001)`	Dirichlet a0 parameter haplotype frequency prior
`--bayesType arg (=singlevariant) Bayesian EM program type (all or`	singlevariant or priorpersite)

General algorithm filtering options:

--checkAllCIGARs arg (=1) include all indels at the position of the call site

--filterReadAux arg: match string for exclusion of reads based on auxilary information

Observation model parameters:

`--pError arg (=0.00050000000000000001)`	probability of a read indel
`--pMut arg (=1.0000000000000001e-05)`	probability of a mutation in the read
`--maxLengthIndel arg (=5)`	maximum length of a _sequencing error_ indel in read [not for `--faster` option]

Library options:

--libFile arg: file with library insert histograms (as generated by --analysis getCIGARindels)

Misc results analysis options:

--compareReadHap: compare likelihood differences in reads against haplotypes

--compareReadHapThreshold arg (=0.5) difference threshold for viewing

--showEmpirical: show empirical distribution over nucleotides

--showCandHap: show candidate haplotypes for fast method

--showHapAlignments: show for each haplotype which reads map to it

--showReads: show reads

--inferenceMethod arg (=empirical): inference method

--opl: output likelihoods for every read and haplotype

dindel1

Overview

[Required] :

[Required] Program option:

[Required] BAM input. Choose one of the following:

[Required for analysis == indels]:

Output options:

parameters for analysis==indels option:

General algorithm parameters:

parameters for --pooled option:

General algorithm filtering options:

Observation model parameters:

Library options:

Misc results analysis options:

[Required] :

[Required] Program option:

[Required] BAM input. Choose one of the following:

[Required for analysis == indels]:

Output options:

parameters for analysis==indels option:

General algorithm parameters:

parameters for --pooled option:

General algorithm filtering options:

Observation model parameters:

Library options:

Misc results analysis options:

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