New User Advice

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 2 comments
ApplyBQSR doesn't recognise my arguments? Answered
- Ali Hudson
- November 10, 2021 15:55
- Edited
0 votes 3 comments
Exclude non variant sites Answered
- Victoria Buswell
- October 27, 2021 15:26
0 votes 1 comment
Using GATK as a genotyper to genotype existing variants Answered
- Ivar Grytten
- October 12, 2021 13:53
0 votes 6 comments
GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases
- HT
- October 01, 2021 05:28
0 votes 4 comments
Mutect2 somatic mutation calling for plant
- Lina Herliana
- September 15, 2021 01:42
0 votes 2 comments
Help with running GATK RNAseq workflow with docker backend and multiple cpus?
- ThyagoLC
- September 02, 2021 15:38
- Edited
0 votes 3 comments
Empty intersection error when applying intervals Answered
- Ran Wei
- August 31, 2021 22:33
0 votes 3 comments
Script for using same GATK tool(s) on multiple sample files Answered
- Youssef Tawfik
- August 01, 2021 16:32
0 votes 1 comment
Creating dictionary for fasta reeference file Answered
- Priyadarshini Thirunavukkarasu
- July 30, 2021 09:24
- Edited
0 votes 1 comment
GQ in jointly genotyped samples Answered
- stelmaria
- July 29, 2021 21:11
0 votes 1 comment
Combining mplileup and haplotypeCaller calls Answered
- Charlotte Her
- July 22, 2021 17:03
0 votes 2 comments
Help with WDL workflow for mutec2? Answered
- Alex Lee
- July 14, 2021 17:01
0 votes 5 comments
looking for panel of normals and allele frequency for hg19 genome build Answered
- elhadi iich
- June 30, 2021 09:47
0 votes 1 comment
picard CollectAlignmentSummaryMetrics required arguments format Answered
- Serge
- June 28, 2021 19:20
0 votes 1 comment
gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) Answered
- Nick Kinney
- June 24, 2021 16:08
0 votes 3 comments

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