Documentation Questions

gatk FilterByOrientationBias Answered
- Nishtha Tanwar
- May 04, 2021 09:15
0 votes 2 comments
GenomicsDBImport java error
- TONG ZHOU TAO
- May 04, 2021 06:33
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
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
ApplyBQSRSpark ApplyBQSR has different results
- AMN
- April 22, 2021 15:40
- Edited
0 votes 3 comments
GC DROPOUT AND AT DROPOUT Answered
- asqt96
- April 22, 2021 13:16
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
every exon junctions in Bam files got softclipped after run SplitNCigarReads Answered
- 이한새
- July 21, 2021 00:49
- Edited
0 votes 4 comments
How does Picard basecalling make decisions on NovaSeq data? Answered
- James Webber
- April 14, 2021 17:12
0 votes 4 comments
If base quality scores set at 2 for clipped regions are restored to the original score with MergeBamAlignment, how will clipped regions not contribute to downstream analyses? Planned
- ISmolicz
- April 07, 2021 15:07
- Edited
0 votes 0 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
GATK 4.2.0.0 Haplotype caller --genotyping_mode DISCOVERY Option Answered
- M.R-E.H
- April 07, 2021 11:30
0 votes 2 comments
Error remove 0x1 from alternate contigs tutorial Answered
- Linda Do
- April 05, 2021 16:18
0 votes 5 comments
CreateSomaticPanelOfNormals BETA tag Answered
- G E
- April 01, 2021 19:38
0 votes 2 comments
Sensitivity analysis for GATK CNV PoN Answered
- Kimal Rajapakshe
- March 29, 2021 21:51
0 votes 1 comment
Mutect2 merge stats Answered
- Saskia
- March 29, 2021 15:05
0 votes 2 comments
Error HaplotypeCaller from alternate contigs tutorial Answered
- Linda Do
- March 25, 2021 20:08
0 votes 4 comments
BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used? Answered
- ISmolicz
- March 24, 2021 18:27
- Edited
0 votes 4 comments
Germline sites in Mutect2 Answered
- G E
- March 19, 2021 04:39
- Edited
0 votes 11 comments
Potential updates to GATK HaplotypeCaller documentation
- Amit
- March 17, 2021 17:00
- Edited
0 votes 1 comment
Alt Contig tutorial question Answered
- Linda Do
- March 15, 2021 05:22
0 votes 7 comments
Three questions about calling CNV in Germline. Answered
- rq m
- March 12, 2021 03:23
- Edited
0 votes 7 comments
Mutect2 panel of normals design Answered
- Jagadheshwar Balan
- March 08, 2021 14:45
0 votes 2 comments
Truth set download page for BQSR Answered
- prasundutta87
- January 29, 2021 11:54
0 votes 2 comments
Converting Reference Genomes from b37 to hg19
- Abhi Agarwal
- December 30, 2020 19:12
0 votes 4 comments
Known Sites for BQSR Answered
- T. Li
- December 07, 2020 22:26
5 votes 5 comments
RADseq/MIGseq denovo SNP calling in tetraploid plants Answered
- Alfons Weig (ARW)
- December 04, 2020 13:02
- Edited
0 votes 3 comments
HaplotypeCaller vcf file analysis Answered
- ziliang
- November 23, 2020 14:18
0 votes 2 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

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