flagger
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mobinasri
Evaluating genome assemblies
Hi, For the files in FLAGGER_HIFI_PROJECTED_SIMPLIFIED_BEDS/ directories, are their cooddinate based on T2T-CHM13 (v.2.0) or T2T-CHM13 (v.1.1)or hg38? For examples, files in here: https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=submissions/e9ad8022-1b30-11ec-ab04-0a13c5208311--COVERAGE_ANALYSIS_Y1_GENBANK/FLAGGER/APR_08_2022/FINAL_HIFI_BASED/FLAGGER_HIFI_PROJECTED_SIMPLIFIED_BEDS/ Thank you!
Hello, I get the following error when I try to run the flagger pipeline. ``` [2024-05-03 07:30:55,44] [error] BackgroundConfigAsyncJobExecutionActor [ddf63c0arunSecPhase.secphase:NA:1]: Error attempting to Execute java.lang.Exception: Failed command instantiation at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:674)...
Hi, I love the concept of your tool, and am wondering if it would be appropriate to use in a more special l case. I want to evaluate haplotype-resolved de-novo...
Hi, Thanks for a great tool! I have a question on the expected coverage you use to input for running fit_model_extra.py. When we have no reason to suspect there should...
Running flagger on the latest version, I get an error in the call_stats step (for both call_stats and call_stats_alt_removed). Previous steps finish successfully. The error is that the perc_only and...
Hello! Do you have any suggestion for generating the biased_high and biased_low files for CHM13v2.0? It basically would require running the analysis you had in the first place on HG002-chrY....
Hi, I would like to run this pipeline in a plant genome. I would like to skip the step4 "incorporation coverage biases in HSats". How I could achieve this if...
Hi, I'd like to install this software locally - is using the docker image the fastest/best way to do that?
- Handle cases when PAF file has secondary and unaligned records - Throw an error when the input bed file is not merged or sorted - Multi-thread reading PAF file
