How To Generate Library File When Using Candidate Indels?

Question

[lyfsa]

Hi All,

I am trying to run dindel with candidate indels from another variant caller. Now I have the -varfile (variant file) but how can I generate the --libFile (library file), which is required in the step 3 of dindel(step 3 mentioned below)

dindel --analysis indels --doPooled --bamFile sample.bam --ref ref.fa --varFile sample.realign_windows.2.txt --libFile sample.dindel_output.libraries.txt --outputFile sample.dindel_stage2_output_windows.2

Thanks

Answer 1

[Istvan Albert]

The file is created in step 1 in the manual by the flag called --analysis from the manual:

Stage 1 We extract indels from the BAM file and simultaneously infer the library insert size distribution using:

dindel --analysis getCIGARindels --bamFile sample.bam --outputFile sample.dindel_output --ref ref.fa

This will produce a file sample.dindeloutput.variants.txt, which contains all candidate indels, and the file sample.dindeloutput.libraries.txt, which contains the insert size distribution for all libraries in the file. If one has multiple BAM files, this command needs to be run for every BAM file separately.

Note: This will produce one library insert size distribution for every BAM file. The user needs to merge these into a single file that can be used with the --libFile option

[lyfsa]

But I am using candidate indels from pindel and using it in dindel. Do I still have to follow step 1 in that case??

[Istvan Albert]

Well the above is the command to generat the libFile and that's what the original question was about. You should do further research on whether the approaches may be mixed as that is a situation that I have not had to deal with yet.

[lyfsa]

Thank you. I will just create the library file using 1st step. This might work. I could not find any other way right now.

[roll]

Hi, Do you know how to merge the libfiles? i am running multiple bam files and i obtained the libfiles for each of my bam but i do not know how to merge them. thanks

Answer 2

[roll]

Hi, Do you know how to merge the libfiles? i am running multiple bam files and i obtained the libfiles for each of my bam but i do not know how to merge them. thanks