New User Advice

Proper way to prepare .bam for MarkDuplicatesSpark Answered
- samuel
- July 06, 2022 06:46
1 vote 3 comments
Unclear why Picard ValidateSamFile is producing an error Answered
- LOIC TALIGNANI
- November 15, 2022 09:51
0 votes 6 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
Find rate of homozygosity Answered
- Joyce Anon
- July 28, 2022 05:12
0 votes 4 comments
Package ‘gsalib’ was removed from the CRAN repository. Answered
- igor
- July 13, 2022 15:56
0 votes 3 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
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
Suggestions to find pathogenic variant Answered
- Joyce Anon
- May 03, 2022 20:57
0 votes 4 comments
Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
- Joyce Anon
- April 25, 2022 06:30
0 votes 20 comments
GATK working, but -ERC command not found Answered
- Ann W
- April 12, 2022 15:06
0 votes 3 comments
Somatic mutation detection in HLA regions using hg38 alt-aware alignments Answered
- Elisabetta Manduchi
- April 12, 2022 15:00
0 votes 5 comments
ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered
- Andrew Erzunov
- April 19, 2022 20:40
- Edited
0 votes 13 comments
Proper references for mutec2 working in tumour-only mode Answered
- Dr Andrzej Kubiak
- April 05, 2022 11:21
0 votes 1 comment
Discordance genotyping Answered
- PierreJus
- March 28, 2022 20:31
0 votes 1 comment
Picard CrosscheckFingerprints not identifying samples from the same individual as a MATCH Answered
- Christopher Sisk
- March 23, 2022 15:01
0 votes 1 comment
WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:40 and possibly subsequent; at least 10 samples must have called genotypes Answered
- Dina Tzur
- March 13, 2022 16:46
0 votes 3 comments
GATK MarkDuplicatesSpark output error Answered
- Bilge Tabak
- March 11, 2022 17:39
0 votes 3 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
What should I do with vcf file now Answered
- mina ming
- February 03, 2022 13:20
- Edited
0 votes 1 comment
ApplyBQSR for somatic mutation detection in HLA regions Answered
- Elisabetta Manduchi
- February 01, 2022 17:07
0 votes 7 comments
Where is my GATK4 ? Answered
- MianQi
- December 20, 2021 10:15
- Edited
0 votes 1 comment
Pileup output of GATK4 vs. GATK3 Answered
- Ran Wei
- December 02, 2021 01:37
0 votes 1 comment
bash: gatk: command not found Answered
- Jeremy Sutherland
- December 01, 2021 19:20
0 votes 2 comments
GATK GenomicsDBImport intervals Answered
- Bekah W
- November 26, 2021 14:23
0 votes 19 comments
rename sample in GVCF file Answered
- Bekah W
- November 23, 2021 22:08
0 votes 3 comments
MarkDuplicates analysis of large wheat chromosomes Answered
- John Baison
- November 11, 2021 11:54
0 votes 2 comments

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