gatk

gatk copied to clipboard

Hello, when I was merging gvcf files, I used CombineGvcfs and GenomicsDBImport respectively. I found that the result files of these two merged files were inconsistent. They scored the allele...

X7xf

## My question I split into 12 chromosomes and parallel multiple jobs at a time. As the picture says, the process occupy just very low(1%) CPU usage per job, and...

GooLey1025

The parameter value is always `false`, so the module is never actually tested by any test case. 

DarioS

TransferReadTags is unable to delete temp files

1

# Bug Report ## Affected tool(s) or class(es) TransferReadTags ## Affected version(s) ``` ❯ gatk --version Using GATK jar /data1/shahs3/users/schrait/envs/bioinfo/share/gatk4-4.6.1.0-0/gatk-package-4.6.1.0-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 /data1/shahs3/users/schrait/envs/bioinfo/share/gatk4-4.6.1.0-0/gatk-package-4.6.1.0-local.jar --version The...

tobsecret

I found a duplicate of this as issue #9101 from February, which said that it was resolved, but we have hit the problem today, May 7. Running gatk 4.6.2.0 using...

emsisson

To reproduce: Conda env with latest GATK: ``` # gatk.yaml channels: - conda-forge - bioconda dependencies: - gatk4 ==4.6.2.0 ``` Input file (`ref.fa`) with 64 positions: ``` >1 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ```...

lczech

PostprocessGermlineCNVCalls outputs wrong genotyped-segments results

1

We have a partial duplication on chr19 (at 0 ~ 30M) in mouse genome, when using gatk to determine the copy number of chr19 using pipeline described in [https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-rare-germline-copy-number-variants](https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-rare-germline-copy-number-variants). The...

DiabloRex

Any function to add originial qualities to a BQSR bam?

1

My institution had a practice of routinely keeping both original and BQSR bam (output from [ApplyBQSR](https://gatk.broadinstitute.org/hc/en-us/articles/360041849571-ApplyBQSR)). We are in process of shifting practice to keep both original qualities (OQ) and...

rajwanir

Hi there, I get the above error while running GenotypeGVCFs on 1000+ samples. GenomicsDB had no issues. ``` GATK version: v4.4.0.0 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 -Xmx84g -Xms84g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true...

aarthi-mohan

Germline CNV calling error: Cannot run DetermineGermlineContigPloidy due to intability to install gcnvkernel

1

Hi, I tried to run DetermineGermlineContigPloidy in cohort mode and it fails: ``` 06:34:40.112 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 06:34:40.152 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression18318423026447352871.so 06:34:40.685...

Urja25