New User Advice

Unclear why Picard ValidateSamFile is producing an error Answered
- LOIC TALIGNANI
- November 15, 2022 09:51
0 votes 6 comments
Where can I download Homo_sapiens_assembly38.haplotype_database.txt
- Sheryl
- November 17, 2022 05:36
0 votes 2 comments
Package ‘gsalib’ was removed from the CRAN repository. Answered
- igor
- July 13, 2022 15:56
0 votes 3 comments
CollectSamErrorMetrics error Answered
- Joe Georgeson
- October 10, 2022 17:41
0 votes 3 comments
no gatk installation
- pedro toruno
- October 04, 2022 19:18
0 votes 0 comments
VariantFiltration issue Answered
- Theresa Saunders
- September 09, 2022 20:41
0 votes 3 comments
Multi-library designs: error proceeding from pre-processing to variant calling
- Sabrina McNew
- August 23, 2022 20:35
0 votes 1 comment
Find rate of homozygosity Answered
- Joyce Anon
- July 28, 2022 05:12
0 votes 4 comments
Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
- Joyce Anon
- April 25, 2022 06:30
0 votes 20 comments
Gatk4 rnaseq germline snps indels json file Answered
- Alan Foley
- May 19, 2022 10:29
- Edited
0 votes 3 comments
GenomicsDB Import issues
- aheritas
- July 15, 2022 15:47
0 votes 1 comment
Proper way to prepare .bam for MarkDuplicatesSpark Answered
- samuel
- July 06, 2022 06:46
1 vote 3 comments
Mutect2 with and without UMI information Answered
- Davy Deng
- June 16, 2021 15:34
0 votes 3 comments
Variant Quality Score Recalibration Answered
- Jakub S
- May 09, 2022 15:27
0 votes 3 comments
Suggestions to find pathogenic variant Answered
- Joyce Anon
- May 03, 2022 20:57
0 votes 4 comments
Somatic mutation detection in HLA regions using hg38 alt-aware alignments Answered
- Elisabetta Manduchi
- April 12, 2022 15:00
0 votes 2 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
How to use WGA Data in picard Answered
- Marcus Varni
- May 03, 2022 23:13
0 votes 3 comments
ValiidateSamFile Error: Mate not found Answered
- Stephen Johnson
- June 17, 2021 14:39
0 votes 13 comments
ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered
- Andrew Erzunov
- April 19, 2022 20:40
- Edited
0 votes 13 comments
Estimate genotype proportions from filtered variants
- Daniel Castañeda Mogollón
- April 05, 2022 05:49
0 votes 5 comments
Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
- Joel Wallenius
- May 02, 2022 10:38
0 votes 1 comment
GATK working, but -ERC command not found Answered
- Ann W
- April 12, 2022 15:06
0 votes 3 comments
Picard CrosscheckFingerprints not identifying samples from the same individual as a MATCH Answered
- Christopher Sisk
- March 23, 2022 15:01
0 votes 1 comment
Discordance genotyping Answered
- PierreJus
- March 28, 2022 20:31
0 votes 1 comment
Proper references for mutec2 working in tumour-only mode Answered
- Dr Andrzej Kubiak
- April 05, 2022 11:21
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

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