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ding-lab / CharGer

Characterization of Germline variants
https://ding-lab.github.io/CharGer/
GNU General Public License v3.0
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something wrong #38

Closed yubau1112 closed 4 years ago

yubau1112 commented 4 years ago

I already installed Charger and run "runDemo.sh", but I get a lot of "Warning" message

charged.demo.log

fernanda-rodrigues commented 4 years ago

Hi @yubau1112

The warning messages you see can be ignored. The should not affect your results. We are currently working on further improvements to this tool and turning off some of these warning statements. Please let us know if you have further concerns.

Fernanda Martins Rodrigues CharGer Team

yubau1112 commented 4 years ago

image

I get so much "Unsupported" message, is right?

yubau1112 commented 4 years ago

clinvar_20200210_1000.vcf.txt

./vep -i clinvar_20200210.vcf --cache tmp --fasta ~/.vep/homo_sapiens/99_GRCh37 -o clinvar_20200210.vep.vcf --force_overwrite --everything --fork 48 --assembly GRCh37 --port 3337 --vcf --format vcf --symbol --terms SO --tsl --dir_plugins /home/yubau/.vep/Plugins/ --af_exac

clinvar_20200210.vep_1000.vcf.txt

charger -f ~/VEP/ensembl-vep/clinvar_20200210.vep.vcf -o clinvar_20200210.vep.charger.l.vcf -l

image

fernanda-rodrigues commented 4 years ago

Hi @yubau1112

Regarding the the "Unsupported" message you see: when you supply CharGer with a VEP annotated file, it looks for the following population allele frequencies in this order: gnomAD, ExAC, and 1000Genomes. It prioritizes gnomAD over ExAC and so on. When CharGer does not find that allele frequency (either because the file is not annotated with that allele frequency or because the variant is not present in that particular database, it looks for the next one in that list). That was a message meant for developing purposes that I forgot to turn off. I will submit an update with that message removed. In summary, you can ignore that message. Your VEP annotation seems perfectly fine, according to the example file you submitted.

Regarding the error you mention in your second post: I was not able to reproduce it. I ran your VEP annotated VCF file through CharGer and I do not receive any errors. May I ask how you installed CharGer? Did you use the conda environment, as recommended? This seems like a python version related issue. CharGer currently requires python 2.7 to run. If your default python version is 3x, it will issue errors like this.

Fernanda Martins Rodrigues CharGer Team

yubau1112 commented 4 years ago

thanks to your reply Yes, I use the conda environment. but I think you are right. I really use python3 maybe this is python version related issue I will try python 2.7

fernanda-rodrigues commented 4 years ago

@yubay1112 The conda environment installation is to create an environment with python2, suitable for CharGer. Make sure that you activate your conda environment prior to running CharGer or that you add the path to charger to your .bashrc file, as instructed. Please let us know if you have any further questions.

yubau1112 commented 4 years ago

I reinstall CharGer step by step:

mkdir CharGer cd CharGer wget https://repo.anaconda.com/archive/Anaconda2-5.2.0-Linux-x86_64.sh bash Anaconda2-5.2.0-Linux-x86_64.sh

Do you accept the license terms? [yes|no] [no] >>> yes

Anaconda2 will now be installed into this location: /home/yubau/anaconda2

[/home/yubau/anaconda2] >>>

Do you wish the installer to prepend the Anaconda2 install location to PATH in your /home/yubau/.bashrc ? [yes|no] [no] >>>yes

Do you wish to proceed with the installation of Microsoft VSCode? [yes|no] >>> no

(finish install anaconda)

conda create --name CharGer python=2.7 conda activate CharGer

(CharGer) [yubau@cmuh-i2 Demo]$ which conda ~/anaconda2/bin/conda (CharGer) [yubau@cmuh-i2 Demo]$ ~/anaconda2/bin/conda --version conda 4.5.4

(CharGer) [yubau@cmuh-i2 Demo]$ which pip ~/anaconda2/envs/CharGer/bin/pip (CharGer) [yubau@cmuh-i2 Demo]$ ~/anaconda2/envs/CharGer/bin/pip --version pip 19.3.1 from /home/yubau/anaconda2/envs/CharGer/lib/python2.7/site-packages/pip (python 2.7)

(CharGer) [yubau@cmuh-i2 Demo]$ python --version Python 2.7.17 :: Anaconda, Inc.

conda install pysam

wget -O CharGer.zip https://github.com/ding-lab/CharGer/archive/master.zip unzip CharGer.zip mv CharGer-master/ CharGer cd CharGer pip install . conda deactivate vim ~/.bashrc

I found: #added by Anaconda2 installer export PATH="/home/yubau/anaconda2/bin:$PATH"

and add export PATH="/home/yubau/anaconda2/envs/CharGer/bin:$PATH"

Re-login Linux terminal

cd /home/yubau/CharGer_test2/CharGer/Demo

conda activate CharGer

(CharGer) [yubau@cmuh-i2 Demo]$ which charger ~/anaconda2/envs/CharGer/bin/charger

previously, I download clinvar_20200210.vcf from clinivar we want to used clinvar_20200210.vcf as test

we download clinvar_20200210.vcf from ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/

and used VEP to annotate vcf file , my VEP command is: ./vep -i clinvar_20200210.vcf --cache tmp --fasta ~/.vep/homo_sapiens/99_GRCh37 -o clinvar_20200210.vep.vcf --force_overwrite --everything --fork 48 --assembly GRCh37 --port 3337 --vcf --format vcf --symbol --terms SO --tsl --dir_plugins /home/yubau/.vep/Plugins/ --af_exac

VEP run finish, result is good, no report any warning or error I upload result on google drive https://drive.google.com/open?id=1YnP6bKxjN1MUBiEUKTPqV-rnQlqXacPe

than, I run charger my charger command is: charger -f clinvar_20200210.vep.vcf -o clinvar_20200210.vep.charger.l.vcf -l --exac-vcf ExAC.r1.sites.vep.vcf --mac-clinvar-tsv clinvar_alleles.multi.b37.tsv --perl /home/yubau/perl --vep-script /home/yubau/VEP/ensembl-vep --vep-config /home/yubau/VEP/ensembl-vep/t/Config.t --vep-cache /home/yubau/.vep --vep-version 99 --vep-output clinvar_20200210_output.charger.vep.vcf --grch 37 --ensembl-release 75 --reference-fasta /home/yubau/.vep/homo_sapiens/99_GRCh37 --fork 48

good, I solve previous problems!

previous problems like (charger -f clinvar_20200210.vep.vcf -o clinvar_20200210.vep.charger.l.vcf -l): image

this time: image file:clinvar_20200210.vep.charger.l.vcf (https://drive.google.com/open?id=1h3-W8GHS7lzQUX4rQwg1Mj1YKUrrKvyr)

image

or, if I execute: charger -f clinvar_20200210.vep.vcf -o clinvar_20200210.vep.charger.x.vcf -x I also can get result!

image

image

file:clinvar_20200210.vep.charger.x.vcf(https://drive.google.com/open?id=1NBNI0d8k6Z-hUC0An0pooUIAc4L8-Po6)

but in CharGer_Classification column have so many Uncertain Significance and not have Pathogenic it's something wrong?

Summary: My boss says charger is a very very very important tool ! In the future, all clinical vcf files will need to use charger to annotate all variants. Ask me to put the test charger first on the work list!

To now, I think, I need to solve 2 things:

  1. Try to make the program not alarm warning (but you say can be ignored)
  2. Make the results believeable

thanks so mach! I will try more

yubau, from taiwan