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> Hi, yes, now I have an answer to all the doubts raised by myself more than one year ago, now. > > 1. For somatic SV detection, is pretty...

I noticed that in the somaticSV.vcf.gz file, the RP and SR of a somatic SV are different in normal and tumor, but I don't understand what this means.

How did you finally solve this problem? I also encountered this problem with MANTA installed by conda.

OK, I know why this error occurred. `convertInversion.py ` The `samtools path` should contain the character samtools，i.e. /home/username/samtools_path/samtools

Hi, I also have the same problem as you. Did you finally solve it?

> Select only reads that take the longest time in the `vg::Watchdog` warnings. Try mapping them with various parameter values (and with a provided fragment length estimate) until the warnings...

When I divided the SVs in each chromosome's sv.vcf.gz file, such as chr2_sv.vcf.gz, into 9 parts and then ran vg construct on each part separately, it was successful! ``` vg...

Thank you for your advice. I have merged SVs from all chromosomes into a single VCF file and am currently running 'vg autoindex --workflow giraffe to build the pan-genome. ```...

> That is often a slow part of the pipeline, especially if you have many samples and a single VCF file. One way to speed it up is to use...

> Firstly, I strongly recommend against using the `-R` option. We do not provide stable behavior for that option, and the results can be unpredictable if you don't know how...