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FilterIntervals will get rid of Y chromosome intervals if there are >50% of female samples

2

## Bug Report ### FilterIntervals gatk FilterIntervals \ -L ${OUTPUT}/bins.interval_list \ --annotated-intervals ${OUTPUT}/bins_annotated.interval_list \ -imr OVERLAPPING_ONLY \ $INPUTHDF5S \ -O ${OUTPUT}/bins_filtered.interval_list ### Description I've been running the gCNV pipeline as...

NotAPoetButACriminal

Document how multi-threading support works in GATK4

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In the classic GATK, walkers had the option to be multi-thread in two different ways: * `NanoSchedulable` for thread-safe `map()` calls. * `TreeReducible` for thread-safe `map()` and `reduce()` calls. Because...

magicDGS

Hi GATK team, I encountered an issue while running the GATK mitochondrial pipeline using Dockstore. The error occured during the step where the pipeline merges merges the aligned BAM file...

jingxiant

Hi GATK Team: I have some questions about the application of PON in GATK Mutect2. I have run some samples with and without PON (other parameters are exactly the same)....

YuanTian1991

0 or 1 based coordinates.

1

Dear Developers, I recently used UCSC hg38 as a reference for gatk mutect2 variant calling. I plan to annotate the variants using VEP but from this[ thread](https://github.com/Ensembl/ensembl-vep/issues/1779#issuecomment-2443806826), VEP supports 1-based...

vappiah

yonghaoy

Hi, everyone! I'm trying to call mutation with Mutect2 with RNA-seq, and my scripts are given below. I simply use one sample as a test, with a prior knowledge that...

Joyjoyjoyc

Hello there, ## Documentation request It would be awesome if each major/minor release of GATK contained benchmarking results run against a truth set. For calling short germline variants, you could...

skchronicles