hrdetect-pipeline
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eyzhao
I've been testing the HRDetect pipeline as well as the scarHRD tool. From what i can tell, both use the same definition of genomic scars when calculating the HRDscore (Ref:...
FileNotFoundError in line 3 of /home/ubuntu/efs/hrdetect-pipeline/projects/pog.smk: [Errno 2] File b'config/pog_custom_cohorts.tsv' does not exist: b'config/pog_custom_cohorts.tsv' 
Hello: Very useful algorithm. Do you know why insertion were not included in the SV signature analysis? There are only four type SVs including Deletion, Insertion, Dup, inter-chromosomal translocation. Any...
Hello, Thanks for getting this package together. I have been trying to install the miniconda version as well as each of the R libraries by itself but I am having...
Take this segments.tsv for illustration, where both segments are > 10Mbp and display different copy number counts but same lohtype: chr start end copy_number lohtype 1 752001 16851000 3 ASCNA...
error message: Miniconda3-latest-Linux-x86_64.sh: line 370: /Users/chenj9/Desktop/Work/bin/hrdetect-pipeline-master/dependencies/miniconda3/pkgs/python-3.7.0-hc3d631a_0/bin/python: cannot execute binary file
Lines 45-48 of calculate_sv_catalog.R implies that the first interSV distance is calculated from the start of the chromosome. The first distance should rather be 0, i.e. c(0, pos[1:n()-1]) should be...
Take this segments.2.tsv file for example chr start end copy_number lohtype 1 752001 16851000 3 ASCNA 1 16858001 17015000 5 ASCNA 1 17017001 17113000 6 ASCNA 1 17114001 72747000 3...
In hrdscore/run_test.R, you are missing the usual instruction gsub("chr","",...) found elsewhere in your script files. As a result, if the "chr" strings are found in file segments.tsv, the TAI score...
From Snakefile: 'Rscript ' + PROJECT_DIR + '/scripts/basic-functions/row_bind_tables.R -i {input} -o {output}' The row_bind_tables.R is missing from the distribution.