New User Advice

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
- Alan Foley
- May 19, 2022 10:29
- Edited
0 votes 1 comment
Variant Quality Score Recalibration
- 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
Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
- Joel Wallenius
- May 02, 2022 10:38
0 votes 1 comment
Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
- Joyce Anon
- April 25, 2022 06:30
0 votes 17 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
Estimate genotype proportions from filtered variants
- Daniel Castañeda Mogollón
- April 05, 2022 05:49
0 votes 5 comments
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
How to provide custom exon-intron annotation source in Funcotator
- Elisabetta Manduchi
- February 18, 2022 13:48
0 votes 4 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
GenotypeGVCFs produces bizarre mapping quality distribution
- Daniel Nondorf
- November 18, 2021 16:49
0 votes 1 comment
GATK Non-model organism variant call SNP site all MQ same value
- Bekah W
- November 13, 2021 14:02
0 votes 1 comment
MarkDuplicates analysis of large wheat chromosomes Answered
- John Baison
- November 11, 2021 11:54
0 votes 1 comment
ApplyBQSR doesn't recognise my arguments? Answered
- Ali Hudson
- November 10, 2021 15:55
- Edited
0 votes 3 comments

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