Provided by: dindel_1.01+dfsg-4build2_amd64 
NAME
dindel - finds of insertions and deletions from short nucleotide sequences
DESCRIPTION
[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
SEE ALSO
The full documentation for dindel you find referenced on
https://sites.google.com/site/keesalbers/soft/dindel
March 2016 DINDEL(1)