gatk

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Misleading error message about multi-sample when no read groups are present

12

HaplotypeCaller checks for `samplesList.numberOfSamples() != 1`. The idea was probably about detecting cases with `> 1`, but when no `@RG` present in the BAM file (i.e. `== 0`), it throws...

aushev

I got 348 samples to analyse their variants. I have read several turorials about how to use gatk to get a population vcf. At the beginning , I tried to...

hougeng

Funcotator keep running but no results or com.google.cloud.storage Connection reset

2

Bug Report Affected tool(s) or class(es) mutect2 and Funcotator Affected version(s) gatk-4.1.8.1 ### Description I tried to use Funcotator to annotate a vcf file. The vcf file had 436 records....

kaixinxiaonvwa-hub

Is Mutect2 reporting variant allele fraction (AF) after adding a 1-read "prior" to the supporting allele depth (AD) values?

3

## Documentation request Mutect2 seems to compute allele fraction (AF) from the allele depth (AD) data *after adding a prior* (which seems to be that it adds 1 read to...

carbocation

DownsampleSam discards NM tag

1

### Affected tool(s) or class(es) gatk DownsampleSam ### Affected version(s) GATK v4.3.0.0 ### Description Input cram file (gs://broad-public-datasets/CHM1_CHM13_WGS2/CHM1_CHM13_WGS2.cram) has NM tags, but the downsampled output file no longer has them....

bw2

It seems that the genotype assignment method used in GenotypeGVCFs is hard-coded to (mostly) `PREFER_PLS` : https://github.com/broadinstitute/gatk/blob/423d106612074aa3480b67b321dc66426b1c600a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java#L377 and the `--genotype-assignment-method` thus has no effect: for example (same data as in...

jan-glx

GenotypeGvcfs mangles the input phase

11

From my review of the code, we have: 1. `GenotypeGvcfs` first [merges overlapping variant contexts](https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java#L271), resulting in genotypes with no-calls. 2. Next, the [samples are re-genotyped](https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java#L272-L273). The problem is that...

nh13

GenomicsDBImport datastore format folder permissions | cause for ERROR: Couldn't create GenomicsDBFeatureReader

17

## Bug Report ### Affected tool(s) or class(es) GenomicsDBImport / GenotypeGVCFs ### Affected version(s) 4.3.0.0 ### Description When creating a GenomicsDB datastore, the created folder has permissions set to 700...

vidprijatelj

java.lang.IllegalStateException: There are no sources based on those query parameters

10

### 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....

ShirelyI

JointGermlineCNVSegmentation skip defragmentation

1

## Bug Report ### Affected tool(s) or class(es) GATK 4.4 JointGermlineCNVSegmentation ### Description I get warning: WARN JointGermlineCNVSegmentation - Multi-sample VCFs found, which are assumed to be pre-clustered. Skipping defragmentation....

georgiiprovisor