Documentation Questions

Collecting chrM reads for mitochondrial analysis & MarkDuplicates
- ana_snc
- May 08, 2023 14:40
- Edited
0 votes 1 comment
Explanation on the HS Penalty metric
- Pierre_Bioinfo
- April 20, 2023 07:51
1 vote 3 comments
Why is the coverage cut abruptly for a region in the bamout file of Mutect2 in comparison to the region in input files?
- ISmolicz
- March 21, 2023 00:15
0 votes 5 comments
Why are full regions removed in the bamout file of Mutect2 when compared to the input files?
- ISmolicz
- April 23, 2023 18:50
- Edited
0 votes 1 comment
gatk SelectVariant identified no snps in the vsf file while it has 63702926 snps
- Vishal Negi
- February 06, 2023 19:24
0 votes 2 comments
SPLICE_SITE specification in Funcotator
- yinxiu Zhan
- March 31, 2023 17:11
0 votes 2 comments
Genotype filtering still write "PASS" in filter field
- Marissa Eronika
- March 21, 2023 15:50
1 vote 7 comments
is --dont-use-soft-clipped-bases discarded in HaplotypeCaller?
- Songming Liu
- March 24, 2023 07:45
0 votes 1 comment
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
2 votes 11 comments
Using haplotype information from high-coverage samples as a prior for Haplotypecaller for other low-coverage samples in the same dataset?
- Nils Paffen
- March 07, 2023 16:43
0 votes 1 comment
Intervals and GenomicsDBImport
- Irbin Manuel Veliz Isidro
- February 17, 2023 09:35
0 votes 2 comments
Picard CollectHsMetrics PCT_TARGET_BASES Output
- michaelmc
- February 23, 2023 17:04
0 votes 2 comments
Funcotator 4.1.2.0 gencode for locatableXSV
- Frank Maiwald
- February 20, 2023 11:55
0 votes 1 comment
error:Argument --emit-ref-confidence
- Rezwan Tariq
- February 22, 2023 10:09
0 votes 0 comments
CallCopyRatioSegments -- how does it work? Answered
- Austin Southard-Smith
- February 10, 2023 20:46
0 votes 3 comments
Why don't I have access to some links? Answered
- Manuel
- January 12, 2022 11:13
0 votes 3 comments
GATK Mutect2 tumor vs. normal sample Answered
- Enrico Cocchi
- October 02, 2020 16:23
0 votes 4 comments
Variables harmonization tutorial for variables collected from Pic-sure from various cohort
- kei_hang_chan
- January 26, 2023 06:18
0 votes 0 comments
Picard's CollectRnaSeqMetrics
- Benli Chai
- January 17, 2023 20:36
0 votes 0 comments
Detailed reason for filtering by FilterMutectCalls
- tan qiang
- January 13, 2023 07:44
0 votes 0 comments
How to specify number of threads while running Mutect2
- Tanay Biswas
- December 21, 2022 05:49
0 votes 0 comments
Should we run MarkDuplicates on PCR-Free Libraries made using PCR-Free Kits to take care of Optical Duplicates ?
- rohit satyam
- July 28, 2020 20:28
- Edited
0 votes 3 comments
BuildBamIndex
- Robert Bremel
- November 08, 2022 20:27
0 votes 4 comments
Best practice trios
- Sheryl
- November 23, 2022 00:58
- Edited
0 votes 0 comments
Java exception: index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
- Julián García-Abadillo
- October 27, 2022 13:37
- Edited
0 votes 2 comments
vcf files for BQSR step Answered
- Varun Gupta
- March 30, 2020 22:13
1 vote 4 comments
mutect2 multi-sample Answered
- zhao shilin
- May 07, 2020 17:27
- Edited
0 votes 35 comments
What does RAW_MQ annotation mean ?
- Robert Baldwin
- July 27, 2022 19:49
0 votes 3 comments
Can't access google cloud it says permission required
- HQ Zhao
- October 27, 2022 02:03
0 votes 2 comments
Report file CreateExtendedIlluminaManifest Report file
- James Gallant
- October 31, 2022 15:28
1 vote 1 comment

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