We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
HaplotypeCaller Memory 3.4.0
I am new to the HaplotypeCaller and have huge problems getting it to run ok. I have WGS re-sequencing bam files with ~30-60 coverage (bam files are >3GB in size). I am running these in ERC mode as suggested, but within minutes, 3/4 are killed by the cluster due to exceeding memory. I am using the following command:
java -Xmx32g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -I $bamfile -minPruning 4 --min_base_quality_score $min_base_qual --min_mapping_quality_score $min_map_qual -rf DuplicateRead -rf BadMate -rf BadCigar -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -R $ref -o $HCdir"."HC.$bamfile".""."g.vcf -ploidy $cohort1_ploidy -stand_emit_conf $stand_emit -stand_call_conf $stand_call --pcr_indel_model NONE "
I have varied the amount of memory I allocate up to -Xmx256 with no improvements, and this seems a bit odd to me? Even adding the minPruning did not seem to improve the situation. I have looked at previous posts and know that HC appears quite memory greedy, but is this normal to this extent?
Many thanks in advance for any pointers.