General Discussion

Hi, i am beginner in bioinformatics and need help in how i can index the <fa ref gene file> to accept it , i tried samtools faidx to make .fai file but It didn't do anything about the problem.
- Mina Ashraf
- March 26, 2023 08:58
0 votes 1 comment
GATK pathseq reference database availability
- Ruiwen Zhou
- March 20, 2023 15:44
0 votes 1 comment
Can DRAGEN-GATK be applied to DNBSEQ?
- rq m
- March 19, 2023 03:02
0 votes 1 comment
variant calling on scRNAseq
- ahlem frigui
- March 17, 2023 10:49
0 votes 1 comment
ukb - Merging Y chromosome VCF file having different number of samples
- Shashank Shekhar Padhi
- March 10, 2023 08:03
0 votes 2 comments
Question about handling genotypes during VCF liftOver from hg38 to hg19 using LiftoverVCF command
- user105689
- March 07, 2023 20:54
0 votes 1 comment
Question on using GATK-DRAGEN (dragmap-os aligner) with Mutect2
- Anand
- March 07, 2023 02:20
- Edited
0 votes 1 comment
Minimum median mapping quality output query
- smk_84
- March 03, 2023 19:42
0 votes 3 comments
Empty, meaningless HaploytypeCaller output
- Daniel Richard
- March 02, 2023 22:49
0 votes 1 comment
MarkDuplicatesSpark only supports singleton fragments and pairs. We found the following group with >2 primary reads
- rohit satyam
- March 02, 2023 11:45
- Edited
0 votes 1 comment
Need help with converting VCF to SEG file for CNV visualization Answered
- Sophia
- March 01, 2023 15:32
0 votes 3 comments
GATK pathseq - viladation BLASTN
- Anna Antonatou
- February 22, 2023 13:51
0 votes 2 comments
VQSR first step do not generate plots
- Yousef_genetics
- February 17, 2023 21:12
0 votes 1 comment
Gene coverage issue in GATK 4.3.0.0 using GRCh38
- Rajesh Kumar Maurya
- February 20, 2023 04:27
- Edited
0 votes 2 comments
java.lang.NullPointerException with GenotypeGVCFs on pooled samples
- Anna Dahlgren
- February 10, 2023 15:53
0 votes 1 comment
Gene annonation from aligned genome with reference
- Nagarajan Raju
- January 30, 2023 18:26
0 votes 0 comments
Extract reads from BAM file that contain specific variant
- DC
- January 29, 2023 19:54
0 votes 0 comments
Error in LiftOverIntervalList
- Ben Oppenheimer
- January 26, 2023 19:18
0 votes 0 comments
base recalibration
- Laurent MANCHON
- January 26, 2023 14:08
0 votes 0 comments
Question about how to run CrossCheckFingerPrints (Haplotype map)
- Uri David Akavia
- January 25, 2023 10:33
0 votes 1 comment
--max-events-in-region in FilterMutectCalls
- Varun Gupta
- January 24, 2023 17:15
0 votes 0 comments
Pipeline for calling human haloplex fastq's with GATK
- Amy Houseman
- January 24, 2023 14:45
0 votes 0 comments
What is RMSMappingQuality formula
- zhang
- January 14, 2023 09:58
- Edited
0 votes 0 comments
No output table for BaseRecalibrator
- Abigail Sequeira
- January 13, 2023 20:05
0 votes 0 comments
What are the plans for Funcotator?
- Pieter Lukasse
- January 11, 2023 13:41
0 votes 2 comments
Exception in thread "main" java.lang.IllegalArgumentException: Do not use this function to merge dictionaries with different sequences in them. Sequences must be in the same order as well
- richard.wei
- January 11, 2023 08:26
0 votes 9 comments
How do I speed up SelectVariants and CountVariants?
- Joe
- January 10, 2023 15:28
0 votes 3 comments
GenomicsDBImport-Syntax error in JSON file
- Tanay Biswas
- January 06, 2023 08:15
0 votes 5 comments
Using 1 available threads, but 32 were requested [Mutect2]
- Juan José Garcés Latre
- December 30, 2022 09:30
0 votes 0 comments
Is it necessory to mention disable-read-filter in Mutect2 somatic calling?
- Tanay Biswas
- December 21, 2022 06:00
0 votes 0 comments

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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.