Hi all,
I am hoping to try out dindel for indel-calling on my NGS data but coming up against some problems getting it to work on both institute's computing cluster and my desktop machine. On the cluster, I downloaded the source code for the latest version (1.01) and modified the MakeFile to point to the version on samtools, and dindel seemed to compile Ok.
However, I cannot seem to follow the basic usage example in the manual. I keep getting directed to the help page but I cannot see which of of the arguments is missing.
/home/mib-cri/software/dindel-1.01-src/dindel --ref hsa_chr17.fa --bamFile Example.bam --outputFile dindel.test --analysis getCIGARindels
Error parsing input options. Usage:
[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 libary insert size
distributions
indels: infer indels
realignCandidates: Realign/reposition candidates in
candidate file
etc....
So I then went and downloaded the same source code onto my desktop and compiled again. By the way, I notice that the file size of the d ...
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