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GATK Joint Germline Variant Calling - FilterVariantTranches - Documentation

bugSomething isn't workingSomething isn't working

Status: Open.

#1946 In nf-core/sarek;

· Eduardo-Auer opened on Jul 29, 2025

Typo in documentation

docs

Status: Open.

#1945 In nf-core/sarek;

· esamorodnitsky opened on Jul 29, 2025

Stop after specified step

questionFurther information is requestedFurther information is requested

Status: Open.

#1944 In nf-core/sarek;

· GCAT01 opened on Jul 23, 2025

ERROR No signature of method: java.lang.Boolean.getFileSystem()

questionFurther information is requestedFurther information is requested

Status: Open.

#1941 In nf-core/sarek;

· pauleanyoung opened on Jul 18, 2025

<code>multiqc</code> report contents when using the <code>--step</code> parameter

Status: Open.

#1926 In nf-core/sarek;

· MahShaaban opened on Jun 18, 2025

Integer 0 value for <code>lane</code> column in samplesheet causes pipeline to break

bugSomething isn't workingSomething isn't working

Status: Open.

#1923 In nf-core/sarek;

· serenalotreck opened on Jun 16, 2025

· 

3.6

Invalid CRAM file: some paired and mapped reads missing from recalibrated CRAM

bugSomething isn't workingSomething isn't working

Status: Open.

#1919 In nf-core/sarek;

· jcslimmer opened on Jun 14, 2025

GATK4_MARKDUPLICATES not respecting --TMP_DIR

bugSomething isn't workingSomething isn't working

Status: Open.

#1918 In nf-core/sarek;

· alexnater opened on Jun 12, 2025

Error in process 'BAM_VARIANT_CALLING_TUMOR_ONLY_LOFREQ:MERGE_LOFREQ' unparsable vcf record with allele R

bugSomething isn't workingSomething isn't working

Status: Open.

#1915 In nf-core/sarek;

· SpikyClip opened on Jun 3, 2025

Work with split chromosome and cram

bugSomething isn't workingSomething isn't working

Status: Open.

#1914 In nf-core/sarek;

· natir opened on Jun 3, 2025

Sarek parabricks gpu test_full: A USER ERROR has occurred: Bad input: Sample HCC1395_HCC1395N is not in BAM header: [sample]

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#1909 In nf-core/sarek;

· sgrossfeld-arcusbio opened on May 29, 2025

· 

3.6

ERROR ~ Failed to publish file

bugSomething isn't workingSomething isn't working

Status: Open.

#1905 In nf-core/sarek;

· DavideGue opened on May 29, 2025