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 2 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

Welcome

GATK Team Out of Office

The GATK team will be out of office during December 9th 2022 to January 9th 2022 in observance of the holidays. We will not be able to answer posts from within this period. If you are still experiencing issues when we are back, please re-post your inquiry.