dindel - finds of insertions and deletions from short nucleotide
sequences
[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')
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 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
Library options:
- --libFile
arg
- file with library insert histograms (as generated by --analysis
getCIGARindels)
[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')
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 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
Library options:
- --libFile
arg
- file with library insert histograms (as generated by --analysis
getCIGARindels)
The full documentation for dindel you find referenced on
https://sites.google.com/site/keesalbers/soft/dindel