GATK GenotypeGVCFs memory issue when including non-variant-sites and using GenomicsDB as input #1901

Activity

1. percyfal commented on May 28, 2025

   

   percyfal

   on May 28, 2025

   Author

   More actions

   For reference, in my local version, I have now separated SelectVariants and GenotypeGVCFs steps. In short, I added a local module modules/local/gatk4/selectvariants (with some modifications compared to the nf-core version, notably the return of the intervals used):

   Local GATK4/SelectVariants

   process SELECTVARIANTS {
       tag "$meta.id"
       label 'process_single'
   
       conda "${moduleDir}/environment.yml"
       container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
           'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
           'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
   
       input:
       tuple val(meta), path(input), path(vcf_idx), path(intervals), path(intervals_index)
       tuple val(meta2), path(fasta)
       tuple val(meta3), path(fai)
       tuple val(meta4), path(dict) // required if input is a GenomicsDB?
   
       output:
       tuple val(meta), path("*.g.vcf.gz")       , emit: gvcf
       tuple val(meta), path("*.g.vcf.gz.tbi")   , emit: gtbi
       tuple val(meta), path("$interval_list"), optional:true, emit: intervallist
       path "versions.yml"		                , emit: versions
   
       when:
       task.ext.when == null || task.ext.when
   
       script:
       def args = task.ext.args ?: ''
       def prefix = task.ext.prefix ?: "${meta.id}"
       def input_command = input.name.endsWith(".vcf") || input.name.endsWith(".vcf.gz") ? "$input" : "gendb://$input"
       def interval = intervals ? "--intervals ${intervals}" : ""
   
   	interval_list = intervals ? intervals : "${prefix}.interval_list"
       def avail_mem = 3072
       if (!task.memory) {
           log.info '[GATK SelectVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
       } else {
           avail_mem = (task.memory.mega*0.8).intValue()
       }
       """
       gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
           SelectVariants \\
           --variant $input_command \\
           --output ${prefix}.g.vcf.gz \\
           --reference $fasta \\
           $interval \\
           --tmp-dir . \\
           $args
   
       cat <<-END_VERSIONS > versions.yml
       "${task.process}":
           gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
       END_VERSIONS
       """
   
       stub:
       def prefix = task.ext.prefix ?: "${meta.id}"
       """
       touch ${prefix}.g.vcf.gz
       touch ${prefix}.g.vcf.gz.tbi
   
       cat <<-END_VERSIONS > versions.yml
       "${task.process}":
           gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
       END_VERSIONS
       """
   }
   

   I modified subworkflows/local/bam_joint_calling_germline_gatk/main.nf to include the following (after GATK4_GENOMICSDB):

       // Map input for GenotypeGVCFs conditional on option --allsites;
       // currently there is a bug in GATK4 which makes it impossible to
       // use GenomicsDB as input to GenotypeGVCFs
       select_variants_in = GATK4_GENOMICSDBIMPORT.out.genomicsdb.join(
           GATK4_GENOMICSDBIMPORT.out.intervallist).map{
               meta, genomicsdb, intervallist -> [ meta, genomicsdb, [], intervallist, [] ]
       }
   
       // Select only the intervals that were used for GenomicsDBImport
       // and convert to gvcf for joint genotyping if --allsites is set
       SELECTVARIANTS(select_variants_in, fasta, fai, dict)
   
       // This step should only be needed if --allsites is set
       ch_vcf = SELECTVARIANTS.out.gvcf.collect()
       ch_tbi = SELECTVARIANTS.out.gtbi.collect()
       ch_intervallist = SELECTVARIANTS.out.intervallist.collect()
       ch_genotypegvcfs_in = ch_vcf
           .join(ch_tbi, failOnDuplicate: true, failOnMismatch: true)
           .join(ch_intervallist, failOnDuplicate: true, failOnMismatch: true)
           .map{
               meta, gvcf, gtbi, intervallist -> [ meta, gvcf, gtbi, intervallist, [] ]
           }
   
       // Joint genotyping performed using GenotypeGVCFs
       // Sort vcfs called by interval within each VCF
       GATK4_GENOTYPEGVCFS(ch_genotypegvcfs_in, fasta, fai, dict, dbsnp.map{ it -> [ [:], it ] }, dbsnp_tbi.map{ it -> [ [:], it ] })
   

   Ideally, the separate SelectVariants step should only be called if a flag (e.g., --all-variants) is set.