MosaicForecast
MosaicForecast copied to clipboard
parklab
A mosaic detecting software based on phasing and random forest
Hi, I have tumor only mutect2 run (with PoN) and I was looking for how to further filter possible germline variants. I found this code `MuTect2-PoN_filter.py`, and I was wondering...
Hi, i'm encountering issue installing mosaicforecast. The following was what i've conducted but it seems conda is stuck at solving environment. Wondering how may i troubleshoot this issue? `conda env...
Modifications made to Snakemake workflow 1. mappability, repeats, segdup tracks, reference FASTA, and desired coverage for model now added as parameters on `config.yaml` for easier modification. 2. fixed an error...
I wrote a converter from the current output format of MosaicForecast to VCF. I tested the converter on the MosaicForecast output files you sent me.
Hello. When i used MF in 2021, upon the genotype prediction steps, i was able to see the prediction to have such categories:- > cat $file.genotype.predictions.refined.300721.bed | cut -f35 |...
In the article, I could find the Variant calling methods of SNVs and indels separately. I found you called SNVs using SAMtools mpileup with mapping quality >20 and base quality...
Hi, I used DeepMosaic to detect mosaic SNVs from low-depth WGS data, because it supports low-depth samples, but DM does not call mosaic INDELs. I would like to detect mosaic...
Hi, I'm getting an error when I run the ReadLevel_Features_extraction.py with my data. It seems to be a very similar to issue #16 so I made sure that all the...
