Javan Okendo

svtype = variant.info.get("SVTYPE", "SV")

2

I am getting the following error and I am not sure how to go around this. I used the following command to annotate the my vcf. `duphold -v macope2_sorted.vcf -b...

svtype = variant.info.get("SVTYPE", "SV")

6

I am getting the following error and I am not sure how to go around this. I used the following command to annotate the my vcf. `duphold -v macope2_sorted.vcf -b...

I am getting the following error even though I have followed the [introduction](https://bioconductor.org/packages/devel/bioc/vignettes/DEP/inst/doc/DEP.html) Error in `.rowNamesDF

AttributeError: module 'py' has no attribute 'io'

1

I am getting the following error when running vcfstats and I do not know how I can go about this error. Can someone help with this: ```bash vcfstats --vcf output_filtered.vcf...

I am getting the following error when I try to install this application. How can I get around this? ``` bash Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error × Preparing...

Program stuck at [IndexRegistry]: Chunking VCF(s) for days

2

I am having a problem running vg mpmap. It has stuck on the `[IndexRegistry]: Chunking VCF(s)` for days. Is there a solution for this problem? ```bash [IndexRegistry]: Checking for phasing...

It is possible to make "known indels" and "dbsnp" databases optional in this pipeline as was done in Sarek?

3

### Description of feature I am working with zebrafish genome and it lacks "known indels" and "dbsnp" databases and I see it is a mandatory requirement in this pipeline. How...

Clarification needed

1

This tools is helping me with my project and I would like to get some clarifications. I know column 1 is the read ID and the second column tells me...

Example analysis of LFQ MS/MS data

1

Do you have example analysis of LFQ MS/MS data?

N E X T F L O W ~ version 19.10.0 Launching `neoflow_db.nf` [kickass_mcnulty] - revision: 96dbe17e38 Format input mapping file: /cbio/users/javanokendo/proteogenomics/example_data/test_vcf_files.tsv! New mapping file: ./test_vcf_files.tsv! executor > local (1)...