Support gnomADe AFs; Updated tests; Abandon Travis

Dockerfile

@@ -1,26 +1,28 @@
 FROM clearlinux:latest AS builder
 
 # Install a minimal versioned OS into /install_root, and bundled tools if any
-ENV CLEAR_VERSION=33980
+ENV CLEAR_VERSION=41780
 RUN swupd os-install --no-progress --no-boot-update --no-scripts \
     --version ${CLEAR_VERSION} \
     --path /install_root \
     --statedir /swupd-state \
     --bundles os-core-update,which
 
 # Download and install conda into /usr/bin
-ENV MINICONDA_VERSION=py37_4.9.2
-RUN swupd bundle-add --no-progress curl && \
-    curl -sL https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -o /tmp/miniconda.sh && \
-    sh /tmp/miniconda.sh -bfp /usr
+ENV MINICONDA_VERSION=py312_24.4.0-0
+RUN curl -sL https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -o /tmp/miniconda.sh && \
+    bash /tmp/miniconda.sh -bup /usr && \
+    rm -f /tmp/miniconda.sh && \
+    conda config --set solver libmamba
 
-# Use conda to install remaining tools/dependencies into /usr/local
-ENV VEP_VERSION=102.0 \
-    HTSLIB_VERSION=1.10.2 \
-    BCFTOOLS_VERSION=1.10.2 \
-    SAMTOOLS_VERSION=1.10 \
-    LIFTOVER_VERSION=377
-RUN conda create -qy -p /usr/local \
+# Use mamba to install remaining tools/dependencies into /usr/local
+ENV VEP_VERSION=112.0 \
+    HTSLIB_VERSION=1.20 \
+    BCFTOOLS_VERSION=1.20 \
+    SAMTOOLS_VERSION=1.20 \
+    LIFTOVER_VERSION=447
+RUN conda create -y -p /usr/local && \
+    conda install -y -p /usr/local \
     -c conda-forge \
     -c bioconda \
     -c defaults \

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2021 Memorial Sloan Kettering Cancer Center
+Copyright 2024 Memorial Sloan Kettering Cancer Center
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

README.md

@@ -1,21 +1,19 @@
 vcf<img src="https://i.giphy.com/R6X7GehJWQYms.gif" width="28">maf
 =======
 
-To convert a [VCF](http://samtools.github.io/hts-specs/) into a [MAF](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format), each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a `Missense_Mutation` close enough to a `Splice_Site`, can be labeled as either in MAF format, but not as both. **This selection of a single effect per variant, is often subjective. And that's what this project attempts to standardize.** The `vcf2maf` and `maf2maf` scripts leave most of that responsibility to [Ensembl's VEP](http://useast.ensembl.org/info/docs/tools/vep/index.html), but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the **extensive support in parsing a wide range of crappy MAF-like or VCF-like formats** we've seen out in the wild.
-
-[![Build Status](https://travis-ci.com/mskcc/vcf2maf.svg?branch=master)](https://travis-ci.com/mskcc/vcf2maf)
+To convert a [VCF](https://samtools.github.io/hts-specs//) into a [MAF](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format), each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a `Missense_Mutation` close enough to a `Splice_Site`, can be labeled as either in MAF format, but not as both. **This selection of a single effect per variant, is often subjective. And that's what this project attempts to standardize.** The `vcf2maf` and `maf2maf` scripts leave most of that responsibility to [Ensembl's VEP](http://ensembl.org/info/docs/tools/vep/index.html), but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the **extensive support in parsing a wide range of crappy MAF-like or VCF-like formats** we've seen out in the wild.
 
 Quick start
 -----------
 
-Find the [latest stable release](https://github.com/mskcc/vcf2maf/releases), download it, and view the detailed usage manuals for `vcf2maf` and `maf2maf`:
+Find the [latest release](https://github.com/mskcc/vcf2maf/releases), download it, and view the detailed usage manuals for `vcf2maf` and `maf2maf`:
 
     export VCF2MAF_URL=`curl -sL https://api.github.com/repos/mskcc/vcf2maf/releases | grep -m1 tarball_url | cut -d\" -f4`
     curl -L -o mskcc-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf mskcc-vcf2maf.tar.gz; cd mskcc-vcf2maf-*
     perl vcf2maf.pl --man
     perl maf2maf.pl --man
 
-If you don't have [VEP](http://useast.ensembl.org/info/docs/tools/vep/index.html) installed, then [follow this gist](https://gist.github.com/ckandoth/61c65ba96b011f286220fa4832ad2bc0). Of the many annotators out there, VEP is preferred for its large team of active coders, and its CLIA-compliant [HGVS formats](http://www.hgvs.org/mutnomen/recs.html). After installing VEP, test out `vcf2maf` like this:
+If you don't have VEP installed, then [follow this gist](https://gist.github.com/ckandoth/4bccadcacd58aad055ed369a78bf2e7c). Of the many annotators out there, VEP is preferred for its large team of active coders, and its CLIA-compliant [HGVS formats](http://www.hgvs.org/mutnomen/recs.html). After installing VEP, test out `vcf2maf` like this:
 
     perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf
 
@@ -49,6 +47,37 @@ After tests on variant lists from many sources, `maf2vcf` and `maf2maf` are quit
 
 See `data/minimalist_test_maf.tsv` for a sampler. Addition of `Tumor_Seq_Allele1` will be used to determine zygosity. Otherwise, it will try to determine zygosity from variant allele fractions, assuming that arguments `--tum-vad-col` and `--tum-depth-col` are set correctly to the names of columns containing those read counts. Specifying the `Matched_Norm_Sample_Barcode` with its respective columns containing read-counts, is also strongly recommended. Columns containing normal allele read counts can be specified using argument `--nrm-vad-col` and `--nrm-depth-col`.
 
+Docker
+------
+
+Assuming you have a recent version of docker, clone the main branch and build an image as follows:
+
+    git clone [email protected]:mskcc/vcf2maf.git
+    cd vcf2maf
+    docker build -t vcf2maf:main .
+    docker builder prune -f
+
+Now you run the scripts in docker as follows:
+
+    docker run --rm vcf2maf:main perl vcf2maf.pl --help
+    docker run --rm vcf2maf:main perl maf2maf.pl --help
+
+Testing
+-------
+
+A small standalone test dataset was created by restricting VEP v112 cache/fasta to chr21 in GRCh38 and hosting that on a private server for download by CI services. We can manually fetch those as follows:
+
+    wget -P tests https://data.cyri.ac/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz
+    gzip -d tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz
+    wget -P tests https://data.cyri.ac/homo_sapiens_vep_112_GRCh38_chr21.tar.gz
+    tar -zxf tests/homo_sapiens_vep_112_GRCh38_chr21.tar.gz -C tests
+
+And the following scripts test the docker image on predefined inputs and compare outputs against expected outputs:
+
+    perl tests/vcf2maf.t
+    perl tests/vcf2vcf.t
+    perl tests/maf2vcf.t
+
 License
 -------
 
@@ -57,4 +86,4 @@ License
 Citation
 --------
 
-    Cyriac Kandoth. mskcc/vcf2maf: vcf2maf v1.6.19. (2020). doi:10.5281/zenodo.593251
+    Cyriac Kandoth. mskcc/vcf2maf: vcf2maf v1.6. (2020). doi:10.5281/zenodo.593251

maf2maf.pl

@@ -16,7 +16,7 @@
 my ( $tum_depth_col, $tum_rad_col, $tum_vad_col ) = qw( t_depth t_ref_count t_alt_count );
 my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count );
 my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele ) = ( "$ENV{HOME}/miniconda3/bin", "$ENV{HOME}/.vep", 4, 5000, 0 );
-my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz", "" );
+my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz", "" );
 my ( $species, $ncbi_build, $cache_version, $maf_center, $max_subpop_af ) = ( "homo_sapiens", "GRCh37", "", ".", 0.0004 );
 my $perl_bin = $Config{perlpath};
 
@@ -41,8 +41,9 @@
     MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH
     ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj
     ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE
-    ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF
-    gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF );
+    ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomADe_AF gnomADe_AFR_AF gnomADe_AMR_AF
+    gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF
+);
 
 # Check for missing or crappy arguments
 unless( @ARGV and $ARGV[0]=~m/^-/ ) {
@@ -382,7 +383,7 @@ =head1 OPTIONS
  --species        Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens]
  --ncbi-build     NCBI reference assembly of variants in MAF (e.g. GRCm38 for mouse) [GRCh37]
  --cache-version  Version of offline cache to use with VEP (e.g. 75, 84, 91) [Default: Installed version]
- --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz]
+ --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz]
  --help           Print a brief help message and quit
  --man            Print the detailed manual
 
@@ -401,7 +402,6 @@ =head2 Relevant links:
 =head1 AUTHORS
 
  Cyriac Kandoth ([email protected])
- Qingguo Wang ([email protected])
 
 =head1 LICENSE
 

maf2vcf.pl

@@ -9,7 +9,7 @@
 use Pod::Usage qw( pod2usage );
 
 # Set any default paths and constants
-my $ref_fasta = "$ENV{HOME}/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz";
+my $ref_fasta = "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz";
 my ( $tum_depth_col, $tum_rad_col, $tum_vad_col ) = qw( t_depth t_ref_count t_alt_count );
 my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count );
 
@@ -357,7 +357,7 @@ =head1 OPTIONS
  --input-maf      Path to input file in MAF format
  --output-dir     Path to output directory where VCFs will be stored, one per TN-pair
  --output-vcf     Path to output multi-sample VCF containing all TN-pairs [<output-dir>/<input-maf-name>.vcf]
- --ref-fasta      Path to reference Fasta file [~/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz]
+ --ref-fasta      Path to reference Fasta file [~/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz]
  --per-tn-vcfs    Specify this to generate VCFs per-TN pair, in addition to the multi-sample VCF
  --tum-depth-col  Name of MAF column for read depth in tumor BAM [t_depth]
  --tum-rad-col    Name of MAF column for reference allele depth in tumor BAM [t_ref_count]
@@ -376,12 +376,11 @@ =head2 Relevant links:
 
  Homepage: https://github.com/ckandoth/vcf2maf
  VCF format: http://samtools.github.io/hts-specs/
- MAF format: https://wiki.nci.nih.gov/x/eJaPAQ
+ MAF format: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format
 
 =head1 AUTHORS
 
  Cyriac Kandoth ([email protected])
- Qingguo Wang ([email protected])
 
 =head1 LICENSE