gatk
gatk copied to clipboard
broadinstitute
Official code repository for GATK versions 4 and up
Hi This is an issue derived from the GATK forum. https://gatk.broadinstitute.org/hc/en-us/community/posts/17996976455067-HaplotypecallerSpark-error?page=1#community_comment_18161302676123 User is having an issue with HaplotypeCallerSpark possibly a traversal issue. This problem was also present in the past...
Added percentage complete and expected time remaining to `ProgressMeter`. This behavior requires a sequence dictionary to be passed to `ProgressMeter`. Connected `GATKTool` to use the new functionality in the case...
In working on #8296 we have discovered that in the `MafOutputRendererConstants.java` there are myriad constants that hard code aliases with the pattern "Gencode_34_hugoSymbol". This can lead to bad behavior if...
GATK version: 4.4.0.0 Crashing in FilterAlignmentArtifacts. Not clear why Command ``` java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx30g -jar /gpfs/data/lab/bin/gatk/gatk-package-4.4.0.0-local.jar FilterAlignmentArtifacts -R /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta -V 60603-bulk.filtered.vcf.gz -I /gpfs/data/lab/projects/Mini/analysis/STR/60603-bulk_results/60603-bulk.cram --bwa-mem-index-image /gpfs/data/lab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta.img -O 60603-bulk.filtered.FAA.vcf.gz...
This is a tool intended to evaluate the performance of genotyping (not sequencing/variant discovery), for example from a genotyping array or imputation pipeline.
### Instructions The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc....
Probably, it must be (x < minReadsOnEachStrand) instead of (x == 0) https://github.com/broadinstitute/gatk/blob/618f3b1fd59145ccab5a5ca6e1cb8f987f118823/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/StrictStrandBiasFilter.java#L34C75-L34C75
The GATK docker image is on samtools 1.7, which is ancient and has several known issues that users have run into (especially with CRAM files). We shoud update to a...
Using GATK jar /root/miniconda3/envs/denovo/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /root/miniconda3/envs/denovo/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar AnalyzeCovariates -before ./sample_analysis/SRR25308851/SRR25308851_before_recal_data.table -after ./sample_analysis/SRR25308851/SRR25308851_after_recal_data.table -plots ./sample_analysis/SRR25308851/SRR25308851_recalibration_plots.pdf 22:13:29.955 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/root/miniconda3/envs/denovo/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 22:13:29.979 INFO AnalyzeCovariates...
EMR - 5.13.0 Spark - 2.3.0 Running on m5.2xlarge 1 Master and 2 Worker nodes. While running Haplotype Caller Spark on EMR, running into the stack overflow error. `[[email protected] gatk]$...
Metadata
Owner
Metadata
Official code repository for GATK versions 4 and up