GACGAMA

I got it to work by using Python 3.6.11: Substitute `conda create -n ledfx` to `conda create -n ledfx python=3.6` Can't make it work with python 3.7 though.

Hi @xihaoli In this case, the Cases_Sum_nHet is defined as the sum of the heterozygous carriers among case samples for each specific gene-function pair, such as gene-plof for example. Is...

@kwdoyle As a follow-up: I agree with you. Score_Stat is related to the direction, but only when looking at individual variants. I counted the variants in each of the binary...

@xihaoli I have figured a way to do that by using R, but I've used the VCF data which is not the best, because the .GDS files are available. Im...

Using an older version of xgboost (1.7.1 and 1.6) I get different errors, which might be more on the bug side. ``` multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File...

I've managed to make it work with version 2.0.3 of xgboost: Starting at line 163 of somatic_xgboost.py: ``` for input_data in pd.read_csv( input_tsv, sep="\t", chunksize=chunksize, low_memory=False ): test_data = ntchange.ntchange(input_data)...

I have no idea exactly where it is because i'm processing in a cluster, but I could try running it and saving the train dataset to explore if you want...

I think I might have found why there are infinite values. Somehow, some SNPs and INDELs are being called while having 0 alternate alleles (DP4), or 0% VAF. I have...

I'm getting the same error with PacBio HiFi reads ` lq_mask:2025-02-10 08:20:55,896:93:INFO:tmp file /scratch4/nsobrei2/ggama1/longread_cnv_sv/longqc/HCC1395BL_TUMOR_BREAST_CANCER_PACBIO_SUBSAMPLED_fastq/analysis/tmp_10.txt was removed. longQC:2025-02-10 08:20:55,897:366:INFO:Summary table /scratch4/nsobrei2/ggama1/longread_cnv_sv/longqc/HCC1395BL_TUMOR_BREAST_CANCER_PACBIO_SUBSAMPLED_fastq/longqc_sdust.txt was made. Traceback (most recent call last): File "/scratch4/nsobrei2/ggama1/conda/.conda/envs/longqc/bin/longQC.py", line...

Hi @lgmgeo I will rerun the data and get the header. Running manually with: ``` cd /home/ggama1/.config/variantconvert/2.0.1 variantconvert config -c GRCh38/* --set GENOME.path=/scratch4/nsobrei2/references/annotsv/AnnotSV_annotations/BreakpointsAnnotations/GCcontent/GRCh38/GRCh38_chromFa.fasta --fill_genome_header variantconvert convert -i file1_annotated.tsv -o file1_annotated.vcf...