Giulio Genovese

Mutect2 (and HaplotypeCaller) version 4.1.3.0 miscounts number of alleles when overlapping reads are present, as if the "--count-reads" was set to true by default

13

I obtain this reproducible issue with gatk 4.1.3.0: First of all, you have to download the mini input.bam file from this dropbox link: https://www.dropbox.com/sh/78rz5wrhu9zkfzh/AACW9ZPhl4WnD-wmAkKcdHT3a?dl=0 Then setup a GATK working environment:...

Workflow failure: "Workflow is making no progress but has the following unstarted job keys"

3

After running a large workflow on GCS with ~2,500 tasks, rather than the workflow transitioning from running to success, I received the following error: ``` "status": "Failed", "failures": [ {...

Cromwell 75 complains about GCS output file not found when delocalizing directories

1

``` $ echo 'version development workflow main { call main { input: s1 = "x", s2 = "y" } output { Array[File] f = main.f } } task main {...

Array[String] suffix(String, Array[X]) not implemented in the development version

6

A very simple WDL: ``` version development task sfx { input { Array[String] x String docker = "ubuntu:20.04" } command > output { Array[String] x_sfx = suffix(".sfx", x) } runtime...

while pulling docker from GCS: Bucket is a requester pays bucket but no user project provided

10

While trying to pull a docker with Cromwell 58, I get the following error: `"message": "Task xxx.xxx:0:1 failed. The job was stopped before the command finished. PAPI error code 2....

write_lines() exposes absolute paths that should not be visible to the docker running the task

4

Here is a very simple WDL (test.wdl): ``` version 1.0 workflow test { input { Array[File] list } call test { input: list = list } } task test {...

bcf_hdr_parse_line() and bcf_hrec_add_key() in vcf.c do not check for INFO and FORMAT keys matching VCF specifications

1

If I attempt to add a header string to a VCF header using `bcf_hdr_append()`, the string gets passed to the function `bcf_hdr_parse_line()` which parses the key and passes it to...

Equivalent of int feof(FILE *stream) for hFILE in htslib/hfile.h

5

How do you test whether you are at the end of an `hFILE`? The simplest way I could come up is the following: ``` if ( hgetc(fp) != EOF )...

I am trying to use the +fixref plugin to fix a VCF after a liftOver operation. I have two issues. The first issue relates to the following code: ``` else...

bcftools isec --complement non-optimal behavior when duplicate variants are present

2

This is a bit of a weird corner case, but if I have a VCF file with two identical variants `chr1 20000 A G`: ``` (echo "##fileformat=VCFv4.2" echo "##contig=" echo...