wham
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zeeev
Structural variant detection and association testing
This PR fixes the issue discussed in https://github.com/zeeev/wham/issues/51 The PR fixes the random number seed to a const (e.g., `10), which results in reproducible output.
Hi, Is ARM64 architecture supported ? Linux and/or MacOS ? I am trying to build the project on Ubuntu 20.04 ARM64 but it fails with: ``` mkdir bin g++ -fstack-protector-all...
When running WHAM-BAM, the resulting VCF has an info-field 'AT', which is a comma-separated list of 15 numerical values; however, I cannot find any information as to what these fields...
Hi! I'm using whamg by export EXCLUDE=GL000207.1,GL000226.1,GL000229.1,GL000231.1,GL000210.1,GL000239.1,GL000235.1,GL000201.1,GL000247.1,GL000245.1,GL000197.1,GL000203.1,GL000246.1,GL000249.1,GL000196.1,GL000248.1,GL000244.1,GL000238.1,GL000202.1,GL000234.1,GL000232.1,GL000206.1,GL000240.1,GL000236.1,GL000241.1,GL000243.1,GL000242.1,GL000230.1,GL000237.1,GL000233.1,GL000204.1,GL000198.1,GL000208.1,GL000191.1,GL000227.1,GL000228.1,GL000214.1,GL000221.1,GL000209.1,GL000218.1,GL000220.1,GL000213.1,GL000211.1,GL000199.1,GL000217.1,GL000216.1,GL000215.1,GL000205.1,GL000219.1,GL000224.1,GL000223.1,GL000195.1,GL000212.1,GL000222.1,GL000200.1,GL000193.1,GL000194.1,GL000225.1,GL000192.1,NC_007605 whamg -e $EXCLUDE -r chr1:10000000-20000000 -a /reference/GRCh38_full_analysis_set_plus_decoy_hla.fa -f sample.bam | perl ./wham/utils/filtWhamG.pl > output.vcf 2> output.err The result is like: #CHROM POS ID...
Hello, I am trying to install whamg with `git clone --recursive https://github.com/zeeev/wham.git; cd wham; make` I have seen a couple of other issues referring to similar problems but I couldn't...
I am struggling having Whamg running for a WGS .bam file. I used [GATKSV/Wham](https://hub.docker.com/r/gatksv/wham) docker image and the following command: ``` whamg \ -c ${chr_list} \ -x 30 \ -a...
I tried to install Whamg on Ubuntu 18.04, I have installed OpenMP and CMake, but when I run ``` git clone --recursive https://github.com/zeeev/wham.git; cd wham; make ``` I got: ```...
i get install by this Fast and dirty install: git clone --recursive https://github.com/zeeev/wham.git cd wham make and i get this problem: `g++ -fstack-protector-all -Wall -DVERSION=\"v1.7.0-311-g4e8c-dirty\" -std=c++0x -Wno-sign-compare -O3 -Isrc/lib -Isrc/bamtools/include...
Hi, I was curious about the suggested workflow for WHAMG on ~1K genomes. My assumption is that this is what you would want to do: 1) Run WHAMG individually on...
We are observing non-deterministic behavior of `whamg` when run multiple times across cloud VMs on the same BAM file, where about 5-10% of calls are different. I see from a...
