GATKSupportTeam
GATKSupportTeam
This error message occurs when removing the network when running GATK in a docker container. GATK tools still run to completion, but the error message is disruptive. ``` $> docker...
Discussed in office hours. Seems to be a bug with --force-output-intervals in GenotypeGVCFs when using GenomicsDB. ---------- This request was created from a contribution made by Zane Swaydan on June...
This request was created from a contribution made by Mark Godek on May 28, 2020 12:43 UTC. Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360067471451-Funcotator-cannot-complete-funcotaion-for-variant-due-to-alternate-allele -- I'm attempting to annotate germline variants after VQSR with Funcotator...
This request was created from a contribution made by Joyce Anon on April 25, 2022 06:30 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/5573282748699-Error-ShouldNeverReachHereException-FuncotationMap-in-FilterFuncotations](https://gatk.broadinstitute.org/hc/en-us/community/posts/5573282748699-Error-ShouldNeverReachHereException-FuncotationMap-in-FilterFuncotations) \-- FilterFuncotations stops with an error. The input file with the...
This request was created from a contribution made by Brian Wiley on March 18, 2022 22:33 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/360073119131-MuTect2-annotations#community\_comment\_4797484535835](https://gatk.broadinstitute.org/hc/en-us/community/posts/360073119131-MuTect2-annotations#community_comment_4797484535835) \-- 394224746911, do you think it would be possible for Broad...
This request was created from a contribution made by Saurabh Parikh on April 27, 2020 01:53 UTC. Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360061866552-Unable-to-replicate-the-spanning-deletions-documentation -- Hello, I am trying to understand GATKs behavior regarding spanning...
This request was created from a contribution made by Francesco Mazzarotto on March 23, 2022 14:16 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/4892502642075-FilterMutectCalls-haplotype-filter-value-assigned-to-variants-with-different-PGT-tag](https://gatk.broadinstitute.org/hc/en-us/community/posts/4892502642075-FilterMutectCalls-haplotype-filter-value-assigned-to-variants-with-different-PGT-tag) \-- Hello, I am using GATK v4.2.5.0 to process tumor-only samples...
This request was created from a contribution made by Diana Robledo on June 23, 2022 10:56 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/6808932798363-Monomorphic-sites-after-GenotypeGVCFs-include-non-variant-sites](https://gatk.broadinstitute.org/hc/en-us/community/posts/6808932798363-Monomorphic-sites-after-GenotypeGVCFs-include-non-variant-sites) \-- Hello, I am using GATKv4.2.6.1 and GATK best practices. I...
This request was created from a contribution made by Duo Xie on August 20, 2022 16:16 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/8235601014427-Issue-when-running-BaseRecalibrator](https://gatk.broadinstitute.org/hc/en-us/community/posts/8235601014427-Issue-when-running-BaseRecalibrator) \-- REQUIRED for all errors and issues: a) GATK version used:v4.2.6.1 ...
This request was created from a contribution made by tc on February 09, 2022 17:49 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/4418364848795-java-lang-IllegalArgumentException-Invalid-interval-in-FuncotateSegments](https://gatk.broadinstitute.org/hc/en-us/community/posts/4418364848795-java-lang-IllegalArgumentException-Invalid-interval-in-FuncotateSegments) \-- Hi, I tried to annotated a called segment file after following...