lohhla

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Hi, I am trying to run your code and am having too many issues. For many of the issues I am changing the code to run more smoothly. But there...

vaksmaz

I am trying to use your program interactively in RStudio as well as through the command line. I seem to be having trouble with the HLA fasta file. I am...

sandrahoffberg

your pipeline have tooooooooooo many bugs,I really don't make sense why you make pipeline in this way

1

Error in regionUniqMappedRegions[[grep(normalName, names(regionUniqMappedRegions), : attempt to select less than one element in get1index Execution halted Could You explain what's this command line going to do? I had already fixed...

Spartanzhao

unable to run lohhla on test data.

2

I have installed and tried to run the program on hpc conda environment on the test data but encounter the following error  I tried to locate where the error...

iichelhadi

Hello，I would like to know how to determine the occurrence of LOH for an HLA allele from the output file. My value of HLA_type1copyNum_withBAFBin and HLA_type2copyNum_withBAFBin are negative.Is the output...

BGI2016

Hi， How could I get the file solutions.txt ? example-file_solutions.txt like this: Ploidy tumorPurity tumorPloidy example_tumor_sorted 2 0.8 2

shzyjbren

Coverage requirements for LOHHLA

1

Hello, What coverage do you recommend to run this tool for Whole Genome Sequencing? Is 30x Normal and 60x Tumor sufficient? Thanks, Ahwan

ahwanpandey

limbo1996

If i set CopyNumLoc an absolute path of a file, will the software generate this file？or need other software to estimate purity and ploidy？ If I set CopyNumLoc FALSE ,it...

Lxb-qqyb

remove full directory path from BAMid in LOHHLAscript.R

2

at https://github.com/mskcc/lohhla/blob/master/LOHHLAscript.R#L676 it should be revised to `BAMid

anoronh4