--- name: "dindel" section: "1" platform: "linux" package: "dindel" version: "1.01-wu1-3+dfsg-1+b1" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/dindel" --- # dindel(1) finds of insertions and deletions from short nucleotide sequences ## 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