Documentation Questions

Converting Reference Genomes from b37 to hg19
- Abhi Agarwal
- December 30, 2020 19:12
0 votes 4 comments
MergeBamAlignment input files? Answered
- Cora Olpe
- November 18, 2020 14:37
0 votes 3 comments
Unix pipe support and SAM fields used in Variant Calling pipeline Answered
- Rocco Gabriele Storace
- November 19, 2020 13:38
0 votes 2 comments
How can I get AF for each sample in GVC JointGenotyping mode? Answered
- Jenifer
- November 19, 2020 08:25
0 votes 3 comments
HaplotypeCaller vcf file analysis Answered
- ziliang
- November 23, 2020 14:18
0 votes 2 comments
Where do I find sample dataset for practice? Answered
- Kountay Dwivedi
- October 24, 2020 17:48
0 votes 2 comments
vcf files for BQSR step Answered
- Varun Gupta
- March 30, 2020 22:13
1 vote 4 comments
How to find or generate common germline variant sites VCF required by GetPileupSummaries
- Antti Koskenalho
- May 27, 2020 06:22
1 vote 4 comments
Map reads to a reference with alternate contigs like GRCH38 using GATK4
- neethukrishna Kausthubham
- July 29, 2020 10:14
0 votes 3 comments
Create Somatic PON threshold Answered
- Pedro Miguel Raposo
- July 31, 2020 14:53
0 votes 1 comment
GATK-CollectVariantCallingMetrics - regarding more information
- Krithika_Subramanian
- August 04, 2020 14:33
0 votes 1 comment
panel of normal hg19 version Answered
- 김성윤
- August 11, 2020 07:38
0 votes 1 comment
How is AC calculated?
- mk
- April 12, 2020 22:30
0 votes 1 comment
GATK CNV interpret Segment_Mean and MEAN_LOG2_COPY_RATIO Answered
- lzhan140
- June 24, 2020 23:04
0 votes 3 comments
What does PCT_MIX from CreateVerifyIDIntensityContaminationMetricsFile mean?
- Lucas Taniguti
- June 21, 2021 13:40
0 votes 2 comments
Calculation method of the global_read_depth.tsv file of the DetermineGermlineContigPloidy tool Answered
- Tintest
- May 20, 2021 14:35
0 votes 7 comments
Confirmation that Mutect2 /haplotype caller only use reads mapped within the active region
- JW
- June 03, 2021 16:19
1 vote 3 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
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
I have question about stats file after using mutect2 Answered
- 황신원
- May 21, 2021 00:56
0 votes 1 comment
What is the difference between "CNVSomaticPairWorkflow.common_sites" and "CNVSomaticPairWorkflow.intervals"? Answered
- Hiro Ama
- May 12, 2021 07:18
0 votes 2 comments
STRANDQ missing from mutect2 vcf records Answered
- Rebecca Halperin
- May 12, 2021 19:26
0 votes 6 comments
GC DROPOUT AND AT DROPOUT Answered
- asqt96
- April 22, 2021 13:16
0 votes 1 comment
VariantRecalibrator latest recommandations Answered
- nhaus
- May 04, 2021 15:48
0 votes 3 comments
gatk FilterByOrientationBias Answered
- Nishtha Tanwar
- May 04, 2021 09:15
0 votes 2 comments
How do adapter sequences not contribute to alignment if the base quality is set to 2 with SamToFastq but BWA-MEM does not consider base quality scores? Answered
- ISmolicz
- April 07, 2021 14:37
- Edited
0 votes 5 comments
What does mutect2 do if two bams are input and --normal-sample is not specified? Answered
- Tyler Borrman
- April 27, 2021 05:07
- Edited
0 votes 1 comment
GenomicsDBImport java error
- TONG ZHOU TAO
- May 04, 2021 06:33
0 votes 1 comment
Determining Optimal Number of Samples to include in Panel of Normal Answered
- Gannon Cottone
- April 16, 2021 16:56
0 votes 2 comments
QualByDepth documentation issue Answered
- Uday Evani
- September 09, 2020 21:38
0 votes 18 comments

Genome Analysis Toolkit

Need Help?

Community Forum

Documentation Questions

Welcome

Didn't find what you were looking for?

Quick Links

Recent GATK News

About the GATK community