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 dindel executable is different on the different environments (3.2 MB on my machine, 2.8 Mb on the computing cluster). When I try and run dindel on my desktop, I don't get an error about the arguments, but an error that seems to imply that I've specified multiple bam files
/home/dunnin01/software/dindel-1.01-src/dindel --ref hsa_chr17.fa --bamFile Example.bam --outputFile dindel.test --analysis getCIGARindels
Can extract the full set of indels from only BAM file at a time.
Why does one compiled version of the program not recognise arguments, and the other complain about the arguments that I do give it?