[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