Documentation Questions

Calling somatic CNVs Answered
- Yasin Uzun
- September 09, 2020 02:34
0 votes 6 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
Known Sites for BQSR Answered
- T. Li
- December 07, 2020 22:26
5 votes 5 comments
CollectAllelicCounts interval_list Answered
- jejacobs23
- May 18, 2020 22:33
1 vote 15 comments
Truth set download page for BQSR Answered
- prasundutta87
- January 29, 2021 11:54
0 votes 2 comments
RADseq/MIGseq denovo SNP calling in tetraploid plants Answered
- Alfons Weig (ARW)
- December 04, 2020 13:02
- Edited
0 votes 3 comments
Does CollectReadCounts Count Fragments or Individual Reads? Answered
- Fong Chun Chan
- July 16, 2021 09:19
- Edited
0 votes 3 comments
every exon junctions in Bam files got softclipped after run SplitNCigarReads Answered
- 이한새
- July 21, 2021 00:49
- Edited
0 votes 4 comments
MarkDuplicates not checking sequences Answered
- Naomie Abecassis
- July 13, 2021 13:35
0 votes 3 comments
Best practice to deal with spanning deletion for downstream analysis Answered
- Degang Wu
- November 05, 2020 03:03
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
GATK VariantEval no concordance between dbSNP and our data Answered
- Pierre_Bioinfo
- May 03, 2021 07:50
0 votes 6 comments
Theorical model for Active region detection Answered
- Naomie Abecassis
- June 22, 2021 14:26
0 votes 6 comments
BQSR --use-original-qualities
- Alijah O'Connor
- April 20, 2020 22:02
- Edited
0 votes 1 comment
ASEReadCounter and overlapping paired reads
- Björn Gylemo
- April 21, 2020 09:07
0 votes 1 comment
ask for target sequencing pipeline code using Mutect2 (gatk 4.1.7.0)
- Zhi Zhang
- April 27, 2020 14:43
0 votes 1 comment
GATK4 Best Practices -- SetNmMdAndUqTags
- Alijah O'Connor
- April 28, 2020 23:37
0 votes 1 comment
What are the initial files required in order to go through the Data Preprocessing, Variant Discovery and IGV phases of Genomic analysis? Answered
- Kountay Dwivedi
- October 21, 2020 15:52
0 votes 3 comments
Difference between GATK Germline CNV Pipeline vs Genome STRiP? Answered
- Muhammad Shoaib Akhtar
- October 29, 2020 08:49
0 votes 8 comments
error-handling-end-exit-codes-in-gatk
- Kshama Aswath
- August 19, 2020 18:50
0 votes 1 comment
GenomAD files for MuTect2 Answered
- Felix
- May 06, 2020 10:18
0 votes 9 comments
ASEReadCounter count each read only once or not
- Qingnan Liang
- September 02, 2020 00:38
0 votes 1 comment
Germline CNV vs HaplotypeCaller/indels
- Heba B abusamra
- September 03, 2020 06:02
0 votes 1 comment
What is the correct step? VQSR and CNNScoreVariants? Answered
- Damian Fermin
- September 04, 2020 17:29
0 votes 2 comments
BQSR Spark: Why Beta? Answered
- Tavi Nathanson
- September 18, 2020 22:51
0 votes 3 comments
After SNPs and INDELs are extracted, can they be recombined later? Answered
- Daniel Westcott
- July 23, 2020 23:09
0 votes 1 comment
Mulitple mapped reads in germline CNV caller (GermlineCNVCaller) Answered
- chrl
- July 29, 2020 07:50
0 votes 1 comment
The base of logarithm for VQSLOD
- Edward David
- August 04, 2020 21:36
0 votes 1 comment
Funcotator misses many Cosmic fields - update possible?
- Tjitske de Vries
- August 13, 2020 08:41
0 votes 1 comment

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