New User Advice

Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
- Joyce Anon
- April 25, 2022 06:30
0 votes 20 comments
GATK GenomicsDBImport intervals Answered
- Bekah W
- November 26, 2021 14:23
0 votes 19 comments
ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered
- Andrew Erzunov
- April 19, 2022 20:40
- Edited
0 votes 13 comments
ValiidateSamFile Error: Mate not found Answered
- Stephen Johnson
- June 17, 2021 14:39
0 votes 13 comments
Steps For GATK-gCNV pipleline on Exome Data
- Y R
- April 03, 2023 15:30
- Edited
0 votes 12 comments
AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three': 'separated fields as numeric values>' did not match read name '2hpf_wt_total_SRR870747.42096'. Answered
- Dina Tzur
- February 06, 2022 12:01
0 votes 11 comments
ApplyBQSR
- Wondessen Ayalew
- February 23, 2023 06:19
0 votes 10 comments
ApplyBQSR for somatic mutation detection in HLA regions Answered
- Elisabetta Manduchi
- February 01, 2022 17:07
0 votes 7 comments
DP for each variant bulk is skewed towards 50 and multiples of 50
- Lauren Fedenia
- April 21, 2021 19:02
0 votes 7 comments
Unclear why Picard ValidateSamFile is producing an error Answered
- LOIC TALIGNANI
- November 15, 2022 09:51
0 votes 6 comments
Using GATK as a genotyper to genotype existing variants Answered
- Ivar Grytten
- October 12, 2021 13:53
0 votes 6 comments
GATK configration
- Wondessen Ayalew
- February 13, 2023 12:28
0 votes 5 comments
Markduplicates
- Atal Saha
- January 03, 2023 16:55
0 votes 5 comments
A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary Answered
- Maha Tageldein
- June 06, 2022 05:03
0 votes 5 comments
Estimate genotype proportions from filtered variants
- Daniel Castañeda Mogollón
- April 05, 2022 05:49
0 votes 5 comments
Help with WDL workflow for mutec2? Answered
- Alex Lee
- July 14, 2021 17:01
0 votes 5 comments
Running best practices workflow step-by-step in command line
- limetree
- June 04, 2021 05:12
1 vote 5 comments
Find rate of homozygosity Answered
- Joyce Anon
- July 28, 2022 05:12
0 votes 4 comments
Suggestions to find pathogenic variant Answered
- Joyce Anon
- May 03, 2022 20:57
0 votes 4 comments
How to provide custom exon-intron annotation source in Funcotator
- Elisabetta Manduchi
- February 18, 2022 13:48
0 votes 4 comments
GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases
- HT
- October 01, 2021 05:28
0 votes 4 comments
Mutect2 wdl interval list and scatter count
- Sheryl
- March 06, 2023 02:19
- Edited
0 votes 3 comments
CollectSamErrorMetrics error Answered
- Joe Georgeson
- October 10, 2022 17:41
0 votes 3 comments
VariantFiltration issue Answered
- Theresa Saunders
- September 09, 2022 20:41
0 votes 3 comments
Package ‘gsalib’ was removed from the CRAN repository. Answered
- igor
- July 13, 2022 15:56
0 votes 3 comments
Proper way to prepare .bam for MarkDuplicatesSpark Answered
- samuel
- July 06, 2022 06:46
1 vote 3 comments
GenomicsDBImport - why "intervals" is required?? Answered
- Jianying Li
- May 25, 2022 00:39
0 votes 3 comments
Gatk4 rnaseq germline snps indels json file Answered
- Alan Foley
- May 19, 2022 10:29
- Edited
0 votes 3 comments
Variant Quality Score Recalibration Answered
- Jakub S
- May 09, 2022 15:27
0 votes 3 comments
How to use WGA Data in picard Answered
- Marcus Varni
- May 03, 2022 23:13
0 votes 3 comments

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