Somatic

Missing Variants from Panel of Normals Answered
- Dave Sims
- July 16, 2021 17:35
- Edited
0 votes 2 comments
GetPileupSummaries Answered
- Mommy Misato
- July 14, 2021 21:17
0 votes 5 comments
Mutect2 PoN - GenomicsDBImport creates empty DB Answered
- Enrico Cocchi
- July 14, 2021 10:37
- Edited
0 votes 15 comments
Created panel of normals returns empty vcf Answered
- Rafael Viana
- July 05, 2021 15:04
0 votes 3 comments
selecting allele depth Mutect2 Answered
- Sonia Wolf
- June 28, 2021 17:39
0 votes 1 comment
The mutect ERROR：Please add an explicit type tag :NAME listing the correct type from among the supported types Answered
- 灵己孟
- June 28, 2021 03:15
0 votes 3 comments
Error while running CreateReadCountPanelOfNormals with gatk-4.1.4.1 Answered
- Alice Shen
- June 10, 2021 07:36
0 votes 3 comments
MuTect2 Mismatch between the reference haplotype and the reference assembly graph path. Answered
- Heejun Jang
- June 07, 2021 02:53
0 votes 1 comment
The output of Mutect2 cannot be accepted by FilterMutectCalls in GATK-4.2.0.0 Answered
- Qihan Long
- June 04, 2021 03:25
- Edited
0 votes 10 comments
The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered
- Ce Wang
- May 25, 2021 06:08
- Edited
0 votes 18 comments
How do I set less stringent germline filtering in Mutect2 / filtermutectcalls, many false negatives Answered
- Tjitske de Vries
- May 21, 2021 09:47
0 votes 1 comment
Mysterious Funcotator issue Answered
- Robert Bremel
- May 21, 2021 01:22
0 votes 7 comments
MergeBamAlignment produces unknown error Answered
- vctrymao
- May 18, 2021 16:19
- Edited
0 votes 4 comments
CollectAllelicCounts- Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded Answered
- rahelp
- May 16, 2021 13:17
0 votes 12 comments
IlluminaBasecallsToSam does not demultiplex NovaSeq barcoded reads Answered
- myourshaw
- May 10, 2021 21:46
- Edited
0 votes 5 comments
java.lang.OutofMemoryError: GC overhead limit exceeded Answered
- Jack Prazich
- May 03, 2021 16:54
0 votes 28 comments
GenomicsDBImport does not support GVCFs with MNPs Answered
- Rodolfo Adrián Arriaga Rivera
- April 23, 2021 16:52
- Edited
0 votes 1 comment
Mutect2
- Sotaro Kanematsu
- April 14, 2021 07:24
0 votes 1 comment
Badly formed genome unclippedLoc: Contig NC_007605 given as location, but this contig isn't present in the Fasta sequence dictionary Answered
- rahelp
- April 12, 2021 13:36
0 votes 7 comments
Why do a clear expected variant not show up in the Mutect2 vcf file Answered
- Nabeel Ahmed
- April 07, 2021 09:13
0 votes 12 comments
CreateSomaticPanelOfNormals ALT allele bug Answered
- G E
- April 02, 2021 15:19
- Edited
0 votes 10 comments
Funcotator data source not correct Answered
- Jamie Xie
- March 29, 2021 20:42
- Edited
0 votes 13 comments
Issue Regarding CNV_Somatic_Pair Workflow
- Hanbing Song
- March 23, 2021 00:02
0 votes 0 comments
Mutect2 failing to produce F1R2.tar.gz files on TCGA bam (tumor-normal pairs) Answered
- TMB
- March 10, 2021 17:29
0 votes 5 comments
Variant called in reads from ArtificialHaplotypeRG Answered
- yingchen69
- March 09, 2021 05:21
0 votes 4 comments
Picard CrosscheckFingerprint: Sequence dictionaries are not the same size Answered
- Doris Fu
- March 08, 2021 20:17
- Edited
0 votes 3 comments
FilterAlignmentArtifacts - only emitting PASS variants Answered
- GE
- March 01, 2021 15:38
0 votes 3 comments
Missing documentation on strict_strand Answered
- GE
- February 28, 2021 19:15
- Edited
0 votes 4 comments
strand_bias filtering is never emitted Answered
- GE
- February 28, 2021 18:11
- Edited
0 votes 7 comments
FilterMutectCalls didn't filtered any variants for my vcf file Answered
- Xiya Song
- February 28, 2021 11:02
0 votes 3 comments

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