.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
.TH DINDEL "1" "March 2016" "" "User Commands"
.SH NAME
dindel \- finds of insertions and deletions from short nucleotide sequences
.SH DESCRIPTION
.SS "[Required] :"
.TP
\fB\-\-ref\fR arg
fasta reference sequence (should be
indexed with .fai file)
.TP
\fB\-\-outputFile\fR arg
file\-prefix for output results
.SS "[Required] Program option:"
.TP
\fB\-\-analysis\fR 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
.SS "[Required] BAM input. Choose one of the following:"
.TP
\fB\-\-bamFile\fR arg
read alignment file (should be indexed)
.TP
\fB\-\-bamFiles\fR arg
file containing filepaths for BAMs to be jointly
analysed (not possible for \fB\-\-analysis\fR=\fI=indels\fR
.PP
[Required for analysis == getCIGARindels]:
Region to be considered for extraction of candidate indels.:
.TP
\fB\-\-region\fR arg
region to be analysed in format start\-end, eg.
1000\-2000
.TP
\fB\-\-tid\fR arg
target sequence (eg 'X')
.SS "[Required for analysis == indels]:"
.TP
\fB\-\-varFile\fR arg
file with candidate variants to be tested.
.TP
\fB\-\-varFileIsOneBased\fR
coordinates in varFile are one\-based
.SS "Output options:"
.TP
\fB\-\-outputRealignedBAM\fR
output BAM file with realigned reads
.TP
\fB\-\-processRealignedBAM\fR arg ABSOLUTE path to script to process realigned BAM
file
.TP
\fB\-\-quiet\fR
quiet output
.SS "parameters for analysis==indels option:"
.TP
\fB\-\-doDiploid\fR
analyze data assuming a diploid sequence
.TP
\fB\-\-doPooled\fR
estimate haplotype frequencies using Bayesian EM
algorithm.
May be applied to single individual and pools.
.SS "General algorithm parameters:"
.TP
\fB\-\-faster\fR
use faster but less accurate ungapped
read\-haplotype alignment model
.TP
\fB\-\-filterHaplotypes\fR
prefilter haplotypes based on coverage
.TP
\fB\-\-flankRefSeq\fR arg (=2)
#bases of reference sequence of indel
region
.TP
\fB\-\-flankMaxMismatch\fR arg (=2)
max number of mismatches in indel
region
.TP
\fB\-\-priorSNP\fR arg (=0.001)
prior probability of a SNP site
.TP
\fB\-\-priorIndel\fR arg (=0.0001)
prior probability of a detected indel
not being a sequencing error
.TP
\fB\-\-width\fR arg (=60)
number of bases to left and right of
indel
.TP
\fB\-\-maxHap\fR arg (=8)
maximum number of haplotypes in
likelihood computation
.TP
\fB\-\-maxRead\fR arg (=10000)
maximum number of reads in likelihood
computation
.TP
\fB\-\-mapQualThreshold\fR arg (=0.98999999999999999)
lower limit for read mapping quality
.TP
\fB\-\-capMapQualThreshold\fR arg (=100)
upper limit for read mapping quality in
observationmodel_old (phred units)
.TP
\fB\-\-capMapQualFast\fR arg (=45)
cap mapping quality in alignment using
fast ungapped method
.IP
(WARNING: setting it too high (>50)
.IP
might result in significant
overcalling!)
.TP
\fB\-\-skipMaxHap\fR arg (=200)
skip computation if number of
haplotypes exceeds this number
.TP
\fB\-\-minReadOverlap\fR arg (=20)
minimum overlap between read and
haplotype
.TP
\fB\-\-maxReadLength\fR arg (=500)
maximum length of reads
.TP
\fB\-\-minCount\fR arg (=1)
minimum number of WS observations of
indel
.TP
\fB\-\-maxHapReadProd\fR arg (=10000000)
skip if product of number of reads and
haplotypes exceeds this value
.TP
\fB\-\-changeINStoN\fR
change sequence of inserted sequence to
\&'N', so that no penalty is incurred if
a read mismatches the inserted sequence
.SS "parameters for --pooled option:"
.TP
\fB\-\-bayesa0\fR arg (=0.001)
Dirichlet a0 parameter haplotype frequency
prior
.TP
\fB\-\-bayesType\fR arg (=singlevariant) Bayesian EM program type (all or
singlevariant or priorpersite)
.SS "General algorithm filtering options:"
.HP
\fB\-\-checkAllCIGARs\fR arg (=1) include all indels at the position of the call site
.TP
\fB\-\-filterReadAux\fR arg
match string for exclusion of reads based on
auxilary information
.SS "Observation model parameters:"
.TP
\fB\-\-pError\fR arg (=0.00050000000000000001)
probability of a read indel
.TP
\fB\-\-pMut\fR arg (=1.0000000000000001e\-05)
probability of a mutation in the read
.TP
\fB\-\-maxLengthIndel\fR arg (=5)
maximum length of a _sequencing error_
indel in read [not for \fB\-\-faster\fR option]
.SS "Library options:"
.TP
\fB\-\-libFile\fR arg
file with library insert histograms (as generated by
\fB\-\-analysis\fR getCIGARindels)
.SS "Misc results analysis options:"
.TP
\fB\-\-compareReadHap\fR
compare likelihood differences in reads
against haplotypes
.HP
\fB\-\-compareReadHapThreshold\fR arg (=0.5) difference threshold for viewing
.TP
\fB\-\-showEmpirical\fR
show empirical distribution over
nucleotides
.TP
\fB\-\-showCandHap\fR
show candidate haplotypes for fast
method
.TP
\fB\-\-showHapAlignments\fR
show for each haplotype which reads map
to it
.TP
\fB\-\-showReads\fR
show reads
.TP
\fB\-\-inferenceMethod\fR arg (=empirical)
inference method
.TP
\fB\-\-opl\fR
output likelihoods for every read and
haplotype
.SS "[Required] :"
.TP
\fB\-\-ref\fR arg
fasta reference sequence (should be
indexed with .fai file)
.TP
\fB\-\-outputFile\fR arg
file\-prefix for output results
.SS "[Required] Program option:"
.TP
\fB\-\-analysis\fR 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
.SS "[Required] BAM input. Choose one of the following:"
.TP
\fB\-\-bamFile\fR arg
read alignment file (should be indexed)
.TP
\fB\-\-bamFiles\fR arg
file containing filepaths for BAMs to be jointly
analysed (not possible for \fB\-\-analysis\fR=\fI=indels\fR
.PP
[Required for analysis == getCIGARindels]:
Region to be considered for extraction of candidate indels.:
.TP
\fB\-\-region\fR arg
region to be analysed in format start\-end, eg.
1000\-2000
.TP
\fB\-\-tid\fR arg
target sequence (eg 'X')
.SS "[Required for analysis == indels]:"
.TP
\fB\-\-varFile\fR arg
file with candidate variants to be tested.
.TP
\fB\-\-varFileIsOneBased\fR
coordinates in varFile are one\-based
.SS "Output options:"
.TP
\fB\-\-outputRealignedBAM\fR
output BAM file with realigned reads
.TP
\fB\-\-processRealignedBAM\fR arg ABSOLUTE path to script to process realigned BAM
file
.TP
\fB\-\-quiet\fR
quiet output
.SS "parameters for analysis==indels option:"
.TP
\fB\-\-doDiploid\fR
analyze data assuming a diploid sequence
.TP
\fB\-\-doPooled\fR
estimate haplotype frequencies using Bayesian EM
algorithm.
May be applied to single individual and pools.
.SS "General algorithm parameters:"
.TP
\fB\-\-faster\fR
use faster but less accurate ungapped
read\-haplotype alignment model
.TP
\fB\-\-filterHaplotypes\fR
prefilter haplotypes based on coverage
.TP
\fB\-\-flankRefSeq\fR arg (=2)
#bases of reference sequence of indel
region
.TP
\fB\-\-flankMaxMismatch\fR arg (=2)
max number of mismatches in indel
region
.TP
\fB\-\-priorSNP\fR arg (=0.001)
prior probability of a SNP site
.TP
\fB\-\-priorIndel\fR arg (=0.0001)
prior probability of a detected indel
not being a sequencing error
.TP
\fB\-\-width\fR arg (=60)
number of bases to left and right of
indel
.TP
\fB\-\-maxHap\fR arg (=8)
maximum number of haplotypes in
likelihood computation
.TP
\fB\-\-maxRead\fR arg (=10000)
maximum number of reads in likelihood
computation
.TP
\fB\-\-mapQualThreshold\fR arg (=0.98999999999999999)
lower limit for read mapping quality
.TP
\fB\-\-capMapQualThreshold\fR arg (=100)
upper limit for read mapping quality in
observationmodel_old (phred units)
.TP
\fB\-\-capMapQualFast\fR arg (=45)
cap mapping quality in alignment using
fast ungapped method
.IP
(WARNING: setting it too high (>50)
.IP
might result in significant
overcalling!)
.TP
\fB\-\-skipMaxHap\fR arg (=200)
skip computation if number of
haplotypes exceeds this number
.TP
\fB\-\-minReadOverlap\fR arg (=20)
minimum overlap between read and
haplotype
.TP
\fB\-\-maxReadLength\fR arg (=500)
maximum length of reads
.TP
\fB\-\-minCount\fR arg (=1)
minimum number of WS observations of
indel
.TP
\fB\-\-maxHapReadProd\fR arg (=10000000)
skip if product of number of reads and
haplotypes exceeds this value
.TP
\fB\-\-changeINStoN\fR
change sequence of inserted sequence to
\&'N', so that no penalty is incurred if
a read mismatches the inserted sequence
.SS "parameters for --pooled option:"
.TP
\fB\-\-bayesa0\fR arg (=0.001)
Dirichlet a0 parameter haplotype frequency
prior
.TP
\fB\-\-bayesType\fR arg (=singlevariant) Bayesian EM program type (all or
singlevariant or priorpersite)
.SS "General algorithm filtering options:"
.HP
\fB\-\-checkAllCIGARs\fR arg (=1) include all indels at the position of the call site
.TP
\fB\-\-filterReadAux\fR arg
match string for exclusion of reads based on
auxilary information
.SS "Observation model parameters:"
.TP
\fB\-\-pError\fR arg (=0.00050000000000000001)
probability of a read indel
.TP
\fB\-\-pMut\fR arg (=1.0000000000000001e\-05)
probability of a mutation in the read
.TP
\fB\-\-maxLengthIndel\fR arg (=5)
maximum length of a _sequencing error_
indel in read [not for \fB\-\-faster\fR option]
.SS "Library options:"
.TP
\fB\-\-libFile\fR arg
file with library insert histograms (as generated by
\fB\-\-analysis\fR getCIGARindels)
.SS "Misc results analysis options:"
.TP
\fB\-\-compareReadHap\fR
compare likelihood differences in reads
against haplotypes
.HP
\fB\-\-compareReadHapThreshold\fR arg (=0.5) difference threshold for viewing
.TP
\fB\-\-showEmpirical\fR
show empirical distribution over
nucleotides
.TP
\fB\-\-showCandHap\fR
show candidate haplotypes for fast
method
.TP
\fB\-\-showHapAlignments\fR
show for each haplotype which reads map
to it
.TP
\fB\-\-showReads\fR
show reads
.TP
\fB\-\-inferenceMethod\fR arg (=empirical)
inference method
.TP
\fB\-\-opl\fR
output likelihoods for every read and
haplotype
.SH "SEE ALSO"
The full documentation for
.B dindel
you find referenced on https://sites.google.com/site/keesalbers/soft/dindel