[Jaap]

Ah Ofcourse. Was confused by the separate alignment files.
Thanks.

[libiyagirl]

In my case, when I was running

$ python makeWindows.py --inputVarFile 1.txt --windowFileFrefix sample.realign_windows--numWindowsPerFile 1000

it says I should specify --windowFilePrefix
why? how to solve this problem?

[libiyagirl]

Please ignore my message, problem solved!

[aos]

Problems installing dindel

Can somebody help?
Executing make produces this list of warnings and errors
(I had to edit the messages to remove the smilies...)

###########################################
make
g++ -o dindel -I/home/aoschmitt/Desktop/samtools-0.1.14/ -Iseqan_library/ -I./ -Wno-deprecated -O3 DInDel.o HapBlock.o HaplotypeDistribution.o ObservationModelFB.o GetCandidates.o Faster.o -L/home/aoschmitt/Desktop/samtools-0.1.14/ -lbam -lz -lboost_program_options -static
/usr/lib/gcc/i486-linux-gnu/4.4.3/../../../../lib/libbam.a(knetfile.o): In function `socket_connect':
(.text+0xa8d): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
DInDel.o : In function `T.12415':
DInDel.cpp: (.text+0x9c2b): undefined reference to `boost :: program_options::validation_error::validation_error(boost: rogram_options::validation_error::kind_t, std::basic_string char

[......]

DInDel.o InDel.cpp .text+0x26f05): more undefined references to `boost: rogram_options: options_description: ptions_description(std::basic_string char, std::char_traits<char>, std::allocator char const&, unsigned int, unsigned int)' follow
collect2: ld returned 1 exit status

[francesconea]

Hello everyone,
I have problems with the very first step of Dindel. I mean, I should give it my "raw" bam files, right? Not merged, not realigned, just sorted.
so, what I actually do is:
dindel --ref ref.fa --outputFile sample.dindel_output --analysis getCIGARindels --region region.interval_list --bamFile sample.bam

and what I got is Error parsing input options. Usage: plus the complete list of options and commands. Where's my mistake?

Thanks in advance,

Francesco

[lshen]

Here is my commands used

#####################
## GB1G
mkdir /data/lshen/sv/yeast2/w303/dindel_GB1G_101
cd /data/lshen/sv/yeast2/w303/dindel_GB1G_101


/home/lshen/bio/dindel-1.01/dindel-1.01 --analysis getCIGARindels --minCount 5 --bamFile ../novo_GB1G_recal_w303a.bam --outputFile novo_GB1G_recal_w303a.dindel_output_minCount5 --ref /data/lshen/sv/yeast/w303.fa





/home/lshen/bio/dindel-0.12/makeWindows.py --inputVarFile novo_GB1G_recal_w303a.dindel_output.variants.txt --windowFilePrefix novo_GB1G_recal_w303a.dindel_output.realign_windows --numWindowsPerFile 5000




nohup /home/lshen/bio/dindel-1.01/dindel-1.01 --analysis indels --doDiploid --bamFile ../novo_GB1G_recal_w303a.bam --ref /data/lshen/sv/yeast/w303.fa --varFile novo_GB1G_recal_w303a.dindel_output.realign_windows.1.txt --libFile novo_GB1G_recal_w303a.dindel_output.libraries.txt --outputFile novo_GB1G_recal_w303a.dindel_stage2_output_windows.1 &


# create glf.list.GB1G.w303.txt:

novo_GB1G_recal_w303a.dindel_stage2_output_windows.1.glf.txt
novo_GB1G_recal_w303a.dindel_stage2_output_windows.2.glf.txt
novo_GB1G_recal_w303a.dindel_stage2_output_windows.3.glf.txt


/home/lshen/bio/dindel-1.01/mergeOutputDiploid.py --inputFiles glf.list.GB1G.w303.txt --outputFile novo_GB1G_w303a_recal.dindel101_all.vcf --refFile=/data/lshen/sv/yeast/w303.fa -s GB1G -f 5

wc -l novo_GB1G_w303a_recal.dindel101_all.vcf

[francesconea]

Hi lshen, and thank you very much for you help
I just tried that, and doesn't work. I tried also to cancel the "minCount" option and...nothing. In addiction, in the usage it says that with "--analysis getCIGARindels" the region is required too... putting it or not doesn't make any difference...in the sense that it just doesn't work.
Any hints?

[lshen]

Just tried again the first command, and no problem. I used novoalign for SAM and generated BAM. Did you tried some example BAM files?



/home/lshen/bio/dindel-1.01/dindel-1.01 --analysis getCIGARindels --minCount 5 --bamFile ../novo_GB1G_recal_w303a.bam --outputFile novo_GB1G_recal_w303a.dindel_output_minCount5 --ref /data/lshen/sv/yeast/w303.fa


## some output:

Reading BAM file: ../novo_GB1G_recal_w303a.bam
Parsing indels from CIGAR strings...
Number of reads read: 1000000
Wrote indels in CIGARS for target chr10 to file novo_GB1G_recal_w303a.dindel_output_minCount5

[francesconea]

Thank you again lshen Just tried that again, but nothing happens (except the usage commands mistycally appearing soon after I enter the command line ). don't really know what to do...

[evani]

@francesconea Were you able to find solution for your problem ? I tried running dindel and ran into the same problem.

Thanks

[lshen]

Now that GATK now has implemented dindel in its UnifiedGenotyper, maybe it's easier to just shift to GATK. It needs some time to get familiar with the (too) powerful GATK, but it is really worthy of trying out.

[evani]

Thanks Ishen, will look into GATK.

BTW, for future reference here is the fix for the Dindel problem.

http://openwetware.org/wiki/User:Lindenb/Notebook/UMR915/20101124

[jbwhitak]

For those getting the "Error parsing input options." with dindel v1.01, downloading the older version of dindel solves the problem (version 0.12).

This version is not available on the dindel webpage, but can be found here as dindel-0.12.tar.gz: https://sites.google.com/site/keesalbers/soft/dindel

This package does not require any installation, so you only need to unzip the tarball and execute stage1 with:
./dindel_x86-64 --analysis getCIGARindels --bamFile <input BAM> --outputFile <output prefix> --ref <path to reference fasta>

[lshen]

But I think the outputs are quite different between these 2 versions and actually some distance from being interchangeable.

[david_2012]

Solution to &quot;Error parsing input options&quot; in dindel

I can second evani on the link (http://openwetware.org/wiki/User:Lin...MR915/20101124), that got the first run of dindel working for me, the decisive part being:
"fixed the bug by changing "bamFiles" to "bamList" in /usr/local/package/dindel-1.01-src/DInDel.cpp (seems to be a bug in BOOST http://lists.boost.org/Archives/boost/2006/01/98811.php )"
After that, you still have to re-make from the source files and then the first run of dindel worked for me.

But I still got the same error for the second run of dindel. So, I now just switched over to the pre-compiled binary, that is available for download on the dindel website, and it all works!