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Is it necessary to do genotype quality filtration after snp calling with GATK
I have whole genome sequencing data from different sources. And the sequencing depth varies greatly among different samples.And I joint-called SNPs with...Last edited by IdaHao0921; 05-14-2024, 01:27 AM. -
Insertions follow reference in vcf file
Hi,
I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret... -
VQSR mixture model and tranches plot doubts (GATK 4.1.7.0)
Hello everyone:
I am processing 74 germline exome sequencing samples of Mexican childhood patients on GATK 4.1.7.0. After VariantRecalibrator... -
GATK: Calling variants on chromosome Y
Hello everyone,
I apologize if this is a stupid question but I'm new to using GATK.
I've searched this forum for an answer but... -
GATK4 (4.1.2.0) Mutect2 --germline-resource option
Hi everybody,
I am new analyzing WES and I try GATK4 workflow for the detection of somatic variants.
I run Mutect2 in tumor-only... -
vcftools and bcftools disagree
Hello,
I'm trying to impute my data using HRC (sanger server). For that I validated and annotated my vcf using GATK and then prepared... -
The N+1 problem in GATK 4
At our place we use GATK (3-series) for germline SNV/INDEL calling in a clinical setup, and we are now considering how to make the move to the new GATK... -
Understanding Read Groups for single end and paired end data
Dear All,
I am new to GATK and very confused regarding "Read Groups". I have fastq files and I will like to add read groups to... -
GATK SNP multi-sample without known SNP database ?
I am working on identifying the SNPs in the genome of an insect which is sequenced in three samples. Following the GATK best practice pipeline i have... -
GATK4, bash script... step CreateSequenceGroupingTSV
Ubuntu, Bash 4.2.25
Hi!
I copy and paste the code about CreateSequenceGroupingTSV and in this way I created a... -
Are you using GATK?
As many of you know, GATK4 Beta is out and we [Broad Team] are excited for the full GATK4 to be released January 9th, 2018. It has been a long time coming... -
What is the best way to find denovo mutations in trios?
I have around 100 trios for which WES was done.
My goal is to find denovo mutations in the child associated with each trios.
So first I... -
SNPs at Interval Boundaries in GATK HaplotypeCaller
I'm using HaplotypeCaller with the -L option, where I explicitly state the interval. I am trying to break my task into pieces and assign it to different... -
Differences in using default and custom interval list (-L) for exome seq?
In exome sequencing, specific interval list (-L) is used by each company to capture particular region. But all exome in the genome will be in particular... -
Pindel and GATK AD Concordance
I was hoping to get some advice on working with the AD field for variants in VCFs produced by Pindel and Pindel2VCF.
My lab has a variant...
