Documentation Questions

Append GenomicsDBimport Answered
- wbsimey
- November 18, 2021 18:26
- Edited
0 votes 3 comments
picard sortvcf: what does it do? Answered
- Thomas Juettemann
- November 09, 2021 17:31
0 votes 6 comments
VariantsToTable GT not extracting correctly Answered
- Asha Mehta
- October 15, 2021 19:59
- Edited
0 votes 1 comment
FilterFuncotations Duplicate key error Answered
- Azza Ahmed
- October 14, 2021 10:53
0 votes 7 comments
haplotypeCaller phasing Answered
- Jeremie Kalfon
- October 05, 2021 15:07
- Edited
0 votes 11 comments
use LearnReadOrientationModel to build artifact-prior.tar.gz Answered
- chenglei
- September 22, 2021 14:48
0 votes 5 comments
How do I call somatic mitochondrial variants? Answered
- Ruiqiao Bai
- September 14, 2021 04:03
0 votes 3 comments
`FilterMutectCalls` for normal only calls Answered
- AMN
- September 10, 2021 16:17
- Edited
0 votes 4 comments
countsN meaning & example Answered
- Mingzhou Fu
- September 08, 2021 15:38
0 votes 2 comments
GATK VariantFiltration Error Answered
- Reza
- September 05, 2021 07:48
0 votes 3 comments
How does GATK HaplotypeCaller behave with respect to deletions that span across a supplied interval in a bed file using -L? Answered
- Rachel Duffin
- August 27, 2021 11:02
0 votes 3 comments
SelectVariants --discordance not working as I expected Answered
- Carlos P Arques
- August 26, 2021 21:10
- Edited
0 votes 3 comments
Interpretation of gene_summary output from DepthofCoverage Answered
- neethukrishna Kausthubham
- August 26, 2021 11:08
0 votes 11 comments
GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered
- Mingzhou Fu
- July 29, 2021 22:42
0 votes 12 comments
Where do I find resources for using FilterVariantTranches with CNN_2D/CNN_1D scores? Answered
- Rodrigo Cabrera
- July 29, 2021 20:00
0 votes 1 comment
Does CollectReadCounts Count Fragments or Individual Reads? Answered
- Fong Chun Chan
- July 16, 2021 09:19
- Edited
0 votes 3 comments
MarkDuplicates not checking sequences Answered
- Naomie Abecassis
- July 13, 2021 13:35
0 votes 3 comments
Where is the list of annotations and annotation groups? Answered
- tedtoal
- July 05, 2021 23:05
0 votes 6 comments
producing strandedness metrics from rnaseq data Answered
- AMN
- July 02, 2021 16:45
0 votes 1 comment
--dbsnp option in HaplotypeCaller and other programs Answered
- gwotto
- July 01, 2021 12:21
0 votes 3 comments
Using -"-allow-old-rms-mapping-quality-annotation-data" to force genotyping gvcf created with old version Answered
- Muriel Gros-Balthazard
- June 25, 2021 08:54
0 votes 1 comment
Theorical model for Active region detection Answered
- Naomie Abecassis
- June 22, 2021 14:26
0 votes 6 comments
MTLowHeteroplasmyFilterTool documentation Answered
- jorgez
- June 11, 2021 12:58
0 votes 7 comments
Is it okay to run multiple instances of BQSR with the -L argument in order to increase the speed of the workflow? Answered
- Jenifer
- May 24, 2021 11:44
0 votes 1 comment
I have question about stats file after using mutect2 Answered
- 황신원
- May 21, 2021 00:56
0 votes 1 comment
Ploidy as an argument in Mutect2 Answered
- Michael Weinstein
- May 21, 2021 00:46
0 votes 1 comment
Calculation method of the global_read_depth.tsv file of the DetermineGermlineContigPloidy tool Answered
- Tintest
- May 20, 2021 14:35
0 votes 7 comments
How do I calculate QD for multiple samples, if all samples are homozygous? Answered
- Martin Grasshoff
- May 19, 2021 16:02
0 votes 1 comment
STRANDQ missing from mutect2 vcf records Answered
- Rebecca Halperin
- May 12, 2021 19:26
0 votes 6 comments
What is the difference between "CNVSomaticPairWorkflow.common_sites" and "CNVSomaticPairWorkflow.intervals"? Answered
- Hiro Ama
- May 12, 2021 07:18
0 votes 2 comments

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