Provided by: dindel_1.01-wu1-3+dfsg-1_amd64 bug

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)