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MarkDuplicates not respecting --TMP_DIR

1

MarkDuplicates and probably other Picard tools don't seem to respect `--TMP_DIR` and keep writing a folder `CSPI.tmpXXXX` to `/tmp`. From the documentation I got the impression that setting `--TMP_DIR /path/to/tmp`...

alexnater

When provided a reference dictionary via --sequence-dictionary, Mutect2 errors out if the "standard" location (sequence.fa -> sequence.dict) isn't present. ### Steps to recreate: Rename reference.dict reference.fa.dict (for example) and provide...

yfarjoun

lbergelson

I am trying to write a nextflow module that uses the NVScoreVariants tool, but I run into the following error whether I use the mentioned container or a seqera container...

famosab

Dear all, I comment on this issue because I have the identical error message but this time in 4.6.2 GATK as found in previous Github tickets for prior versions. Here...

Honeyglitch

Changes the behavior of SVStratify when a variant belongs to more than one stratification group: - Changes the `STRAT` field to a list type so that multiple groups can be...

mwalker174

Requester pays access issue in Terra workspace

1

Hi! I am trying to use the GATK mitochondrial pipeline on All of US data (cloud based on a Terra workspace) but keep running into the same errors as this...

nityajain2002

Output exit result to stderr instead of stdout to allow pipelines

5

fix #5790, #7080 Hi! The exit codes from picard tools are written to stdout which messes up pipelines. In my case, I want to be able to pipe MarkDuplicates to...

pontushojer

Hi GATK, We appear to have run in to a very rare corner case in `CombineGVCFs` that causes it to produce incorrect output. Unfortunately our input data is clinical, so...

drtconway

test yossi's fasta change

3

lbergelson