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#Annotate a vcf file with atext file how to#
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#Annotate a vcf file with atext file software#
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To achieve such statistics, one can run the following commands substituted with specific content. This behavior is desirable by the users who are interested in understanding population PGx and specifically obtaining PGx frequencies (named alleles, diplotypes, or metabolizer phenotypes) in their cohort. PharmCAT users can run the individual components of the PharmCAT on multiple samples in a similar manner to how a user runs the whole PharmCAT. To incorporate outside PGx calls with PharmCAT for multiple samples, the users have to prepare the outside PGx calls of each sample in separate files and supply the individual file as outside calls to the PharmCAT. The output is a set of PGx reports in HTML format named as “pharmcat.html”. " $SINGLE_SAMPLE ".vcf \ -o results/pharmcat_all/ -f pharmcat. Java -jar pharmcat-1.6.0-all.jar \ -vcf results/pharmcat_ready/pharmcat_ready. # running multiple samples for SINGLE_SAMPLE in $( cat data/test_get-rm_samples.txt ) do # always use the latest PharmCAT We recommend the users to still run the PharmCAT VCF preprocessor to ensure the appropriate variant representation format, which can be achieved by the following command and the complete commands can be found in PharmCAT-tutorial/src/02_VCF_preprocessing.sh. If your genetic data is already stored in single-sample VCFs, you are one step closer to running the PharmCAT. Preprocessing case 1 - single-sample VCFs

#Annotate a vcf file with atext file full#

For full commands and a thorough walk-through, please check out the PharmCAT tutorial GitHub repo, specifically src/02_VCF_preprocessing.sh. The following cases provide quick exemplary codes for different types of input VCFs. If not, please check out Preprocessing VCF Files for PharmCAT.Ī separate PharmCAT tutorial GitHub repository provides exemplary commands working with real genetic data sets. We presume that you have familiarized yourself with using the PharmCAT VCF preprocessor. The scripts to run the PharmCAT on the Stanford Sherlock is written in shell programming language, which can be easily adapted to another HPC environment supported by a different job scheduler. The job was run on the Stanford Sherlock, a High-Performance Computing (HPC) cluster which uses Slurm as an open-source resource manager and job scheduler. This part uses the VCFs on multiple GeT-RM samples generated from the 30x high-coverage WGS sequencing performed by the New York Genome Center (NYGC).

Extracting the PharmCAT Phenotyper JSON data into a TSV file.

Extracting the PharmCAT Named Allele Matcher JSON data into a TSV file.

Extracting PharmCAT JSON content into TSV.

Phenotyper - use the Named Allele Matcher JSON data.

Preprocessing case 3 - multi-sample VCF divided by chromosome or into consecutive genetic blocks.

Preprocessing case 2 - multi-sample VCF.

Preprocessing case 1 - single-sample VCFs.

Example using the Stanford Sherlock HPC.

#Annotate a vcf file with atext file how to#

This technical documentation shares two concrete examples of how to use PharmCAT to batch process multiple samples in a High-Performance Computing (HPC) environment. The fast runtime of the PharmCAT enables the users to batch-annotate VCFs, with help from as few as one simple additional script, from the scale of a few dozen samples to a biobank-scale of cohort in an efficient manner. However, PharmCAT can generate a PGx report in the matter of seconds for a preprocessed VCF. If a multi-sample VCF is provided, only the first sample will be annotated.

#Annotate a vcf file with atext file download#

Please cite the VarAFT paper JP Desvignes & al Nucleic Acids Research, gky471, as well as ANNOVAR (PMID:20601685), UMD-Predictor (PMID: 26842889) and HSF (PMID: 19339519) papers if you used them in your research papersīy clicking on the download button you accept this licence.As of March 2022, PharmCAT only takes a single-sample VCF.

#Annotate a vcf file with atext file software#

For more information on how to obtain a commercial license please contact liability for software usage is assumed.

You are required to purchase a license to UMD-Predictor and HSF from GENOMNIS.

For more information on how to obtain a commercial license please go to.

You are required to purchase a license to ANNOVAR from BIOBASE.

For more information on how to obtain a commercial license please go to

For VarAFT please contact You are required to purchase a license for KEGG.

VarAFT is freely available for academic and non-profit use only. The rights to adapt, translate, arrange, correct and, more generally, modify the VarAFT Software are exclusively reserved, at any time and in any place, to AMU and the developers. You shall not duplicate or transfer the VarAFT Software, in whole or in part, in whatever media or manner (electronic format, handwriting process or other), including but not limited to, through copies, downloads, research systems or information storage, for any purpose, without AMU's prior written approval.