Jérémie Kalfon

Hey, no I did not. I have installed it and stil have the same kind of error

same here...

using only "spliceai alfa cscape civic mavedb uniprot loftool fitcons". it works so it must come from one of "dann dida encode_tfbs funseq2 genehancer gwas_catalog pharmgkb provean revel chasmplus"

this happens while running the command ``` java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx15500m\ -jar /root/gatk.jar Mutect2 -R gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta\ -I gs://cclebams/hg38_wes/CDS-00rz9N.hg38.bam -tumor BC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE --germline-resource gs://gcp-public-data--gnomad/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz\ -pon gs://gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz\ -L gs://fc-secure-d2a2d895-a7af-4117-bdc7-652d7d268324/7a157f4a-7d93-4a3e-aaf4-c41833463f5a/Mutect2/3be8ce8e-1075-4063-bc43-6f61e386c3f5/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0000-scattered.interval_list\ -O output.vcf.gz...

Hello, Any updates on this? This seems like an important debug because most people that would want to look at germlines would likely also be interested in having a GVCF...

I am getting the same error... it might be caused by something else?

Hello @davidbenjamin, Any news on this? Can you reproduce on your end?

I am running `v4.2.4.0` and still have the issue. It seems that `mutect2` is doing the wrong thing of separating the `AS_FilterStatus` for different allele using `|` and listing many...

Yes we made a workflow on Terra to debug this: https://dockstore.org/workflows/github.com/broadinstitute/depmap_omics/omics_mutect2:dev?tab=files this is the fix_mutect2.wdl file I believe

Yes I read this document but it still doesn't make sense to me either.. i was thinking of using a tool such as `bcftools +setGT` to set the right GT...