Polysolver software is developed by the Broad Institute. Availability and running instructions for the most current version are described here. This version is preferred.
This fork of Polysolver is a minor modification on jason-weirather/hla-polysolver, which 1) was based on Polysolver 1.0; 2) was modified under Polysolver's BSD-style License; and 3) does not produce exactly the same HLA haplotype calls as the example file included with Polysolver. Most differences were very minor, occurring in the 7th and 8th digits, with one difference in the 4th digit of the HLA-B allele. It should be noted that this work is not affiliated with Polysolver or the Broad Institute, and my work is free to use, reuse and modify under Apache License 2.0. See LICENSE file for licenses of software dependencies.
The purpose of this update of hla-polysolver is to: 1) handle any genome build (hg18/GRCh36, hg19/GRCh37, or hg38/GRCh38); 2) tolerate presence or absence of 'chr' in the chromosome specification of bam files; and 3) like jason-weirather/hla-polysolver, provide HLA haplotype "winner" files for loss of heterozygosity analysis by LOHHLA software (McGranahan et al). As such, it provides one part of a Polysolver-LOHHLA pipeline.
If you are using hla-polysolver in any form, you are requested to cite the original paper by Shukla et al.
- allow user to specify any of the last three genome builds (hg18/GRCh36, hg19/GRCh37, or hg38/GRCh38)
- handle bam files with or without 'chr' in chromosome names
- removed hardwiring of HLA allele fasta file and index; user can provide an alternate. For consistency, the user can use the same allele file for other pipelines such as LOHHLA.
- HLA allele unique sequence file, allele IDs file, and SAM header file are all now generated on the fly from the allele fasta file
Anaconda provides a package incorporating jason-weirather/hla-polsolver 1.0.0. Install and test it before overwriting with this fork. Disclaimer: as with any installation, success here may require supplying additional prerequisites specific to your system either at the level of the operating system or as conda packages. This is left as an exercise for the user.
Set up your conda channels in ~/.condarc:
channels:
- defaults
- bioconda
- conda-forge
- vacation
Create a separate environment for polysolver to isolate its many old dependencies. Then activate and set the perl5 path.
$ conda create -n polysolver -c vacation hla-polysolver
$ conda activate polysolver
(polysolver)$ export PERL5LIB="$CONDA_PREFIX/lib/perl5/5.22.0/"
Get the github repository. You will access test bams and winner files now, and later use it to overwrite hla-polysolver in your conda installation
(polysolver)$ git clone https://github.com/louievdl/hla-polysolver.git
Run tests using anaconda's polysolver and bams from hla-polysolver repo. Increase java memory beforehand if necessary.
The first script, shell_call_hla_type is the only strictly-necessary script for a LOHHLA pipeline, as it produces the winner files required by LOHHLA. It successfully processes the test files without modification.
The second script, shell_call_hla_mutations_from_type, to run successfully, requires minor modification, running muTect specifically under java version 7.
The third script, shell_annotate_hla_mutations runs on the test files without error.
(polysolver)$ export _JAVA_OPTIONS="-Xmx1g" && shell_call_hla_type hla-polysolver/test/test.bam Unknown 1 hg19 STDFQ 0 hla-polysolver/output
(polysolver)$ export _JAVA_OPTIONS="-Xmx1g" && shell_call_hla_mutations_from_type hla-polysolver/test/test.bam hla-polysolver/test/test.tumor.bam hla-polysolver/output/winners.hla.txt hg19 STDFQ hla-polysolver/output
(polysolver)$ shell_annotate_hla_mutations indiv hla-polysolver/output
Results will be in the hla-polysolver/output folder.
- Description
1.1 POLYSOLVER
1.2 POLYSOLVER-based mutation detection
1.3 Annotation of mutations - Installation
- Testing
3.1 POLYSOLVER
3.2 POLYSOLVER-based mutation detection
3.3 Annotation of mutations - Running
4.1 POLYSOLVER
4.2 POLYSOLVER-based mutation detection
4.3 Annotation of mutations
This software package consists of 3 main tools:
1.1 POLYSOLVER (POLYmorphic loci reSOLVER)
This tool can be used for HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (HLA-A, -B, -C).
Script: shell_call_hla_type
Input parameters:
-bam: path to the BAM file to be used for HLA typing
-race: ethnicity of the individual (Caucasian, Black, Asian or Unknown)
-includeFreq: flag indicating whether population-level allele frequencies should be used as priors (0 or 1)
-build: reference genome used in the BAM file (hg18 or hg19)
-format: fastq format (STDFQ, ILMFQ, ILM1.8 or SLXFQ; see Novoalign documentation)
-insertCalc: flag indicating whether empirical insert size distribution should be used in the model (0 or 1)
-outDir: output directory
Output:
winners.hla.txt: file containing the two inferred alleles for each of HLA-A, HLA-B and HLA-C
1.2 POLYSOLVER-based mutation detection
This tool works on a tumor/normal pair of exome BAM files and inferred mutations in the tumor file. It assumes that POLYSOLVER has already been run on the normal BAM.
Script: shell_call_hla_mutations_from_type
Input parameters:
-normal_bam_hla: path to the normal BAM file
-tumor_bam_hla: path to the tumor BAM file
-hla: inferred HLA allele file from POLYSOLVER (winners.hla.txt or winners.hla.nofreq.txt)
-build: reference genome used in the BAM file (hg18 or hg19)
-format: fastq format (STDFQ, ILMFQ, ILM1.8 or SLXFQ; see Novoalign documentation)
-outDir: output directory
Output:
call_stats.$allele.out: Mutect output for each inferred allele in winners.hla.txt
$allele.all.somatic.indels.vcf: Strelka output for each inferred allele in winners.hla.txt
1.3 Annotation of mutations
This tool annotates the predicted mutations from (ii) with gene compartment and amino acid change information
Script: shell_annotate_hla_mutations
Input parameters:
-indiv: individual ID, used as prefix for output files
-dir: directory containing the raw call files (Mutect: call_stats*, Strelka: *all.somatic.indels.vcf). Also the output directory
Output:
(a). Mutect $indiv.mutect.unfiltered.nonsyn.annotated - list of all unfiltered mutations $indiv.mutect.filtered.nonsyn.annotated - list of cleaned non-synonymous mutations $indiv.mutect.filtered.syn.annotated - list of cleaned synonymous changes $indiv.mutect.ambiguous.annotated - list of ambiguous calls. This will generally be empty (save for the header). It will be populated if the same mutation (ex. p.A319E) is found in two or more alleles in the individual, with the same allele fractions. In such cases one allele is randomly chosen and included in the .nonysn.annotated file while the complete list of alleles is listed in the .ambiguous.annotated file. If the ethnicity of the individual is known, an alternate method would be to pick the allele with the highest frequency.
(b). Strelka $indiv.mutect.unfiltered.nonsyn.annotated - list of all unfiltered indels (as detected by Strelka) $indiv.strelka_indels.filtered.annotated - list of cleaned indels (as detected by Strelka) $indiv.strelka_indels.ambiguous.annotated - see description of $indiv.mutect.ambiguous.annotated in (a). above
The POLYSOLVER suite of tools depends upon the following packages and utilities:
Samtools (http://samtools.sourceforge.net/) GATK (https://www.broadinstitute.org/gatk/download) Novoalign (http://www.novocraft.com/main/downloadpage.php) Perl modules ((http://www.cpan.org/modules/INSTALL.html)
- Math::BaseCalc
- List::MoreUtils
- List::Util
- Parallel::ForkManager
- POSIX
- Dumpvalue
- Data::Dumper Bioperl (http://www.bioperl.org/wiki/Installing_BioPerl) Mutect (http://www.broadinstitute.org/cancer/cga/mutect_download) Strelka (https://sites.google.com/site/strelkasomaticvariantcaller/home/download)
Also make changes to the config.sh file to set up the following environmental variables
-PSHOME: POLYSOLVER home directory -SAMTOOLS_DIR: directory containing the samtools executable -JAVA_DIR: directory containing the JAVA executable -NOVOALIGN_DIR: directory containing the Novoalign executables -GATK_DIR: directory containing the GATK jar files -MUTECT_DIR: directory containing the Mutect executable (for POLYSOLVER-based mutation detection only) -STRELKA_DIR: directory containing the Strelka (for POLYSOLVER-based mutation detection only)
The following command should make the necessary changes prior to running the tools (assuming the tcsh shell):
source scripts/config.sh
Your installation can be tested by running the following command from $PSHOME:
3.1 POLYSOLVER
scripts/shell_call_hla_type test/test.bam Unknown 1 hg19 STDFQ 0 test
If successful, the following command should not yield any differences:
diff test/winners.hla.txt test/orig.winners.hla.txt
3.2 POLYSOLVER-based mutation detection
scripts/shell_call_hla_mutations_from_type test/test.bam test/test.tumor.bam test/winners.hla.txt hg19 STDFQ test
If successful, the following command should not yield any differences:
diff test/call_stats.hla_b_39_01_01_02l.out test/orig.call_stats.hla_b_39_01_01_02l.out
3.3 Annotation of mutations
scripts/shell_annotate_hla_mutations indiv test
If successful, the following command should not yield any differences:
diff test/indiv.mutect.filtered.nonsyn.annotated test/orig.indiv.mutect.filtered.nonsyn.annotated
The tools can be run using the following commands:
4.1 POLYSOLVER
$PSHOME/scripts/shell_call_hla_type </path/to/bam> </path/to/output_directory>
example:
$PSHOME/scripts/shell_call_hla_type test/test.bam Unknown 1 hg19 STDFQ 0 test
4.2 POLYSOLVER-based mutation detection
$PSHOME/scripts/shell_call_hla_mutations_from_type </path/to/normal_bam> </path/to/tumor_bam> </path/to/winners.hla.txt> </path/to/output_directory>
example:
$PSHOME/scripts/shell_call_hla_mutations_from_type test/test.bam test/test.tumor.bam test/winners.hla.txt hg19 STDFQ test
4.3 Annotation of mutations
$PSHOME/scripts/shell_annotate_hla_mutations <prefix_to_use> </path/to/directory_with_mutation_detection_output>
example:
$PSHOME/scripts/shell_annotate_hla_mutations indiv test