GATK 3.8 is not working and difficult to find command line for GATK4 can anybody help me with it?

18 December 2019 1 8K Report

I am analysing Whole exome sequencing data using GATK but GATK 3.8 is not working , also I am unable to find commands for GATK 4, Could any one suggest or share pipeline for WES analysis Pipeline.

Sureshkumar v.

Bipin Raj Shekhar

Try this https://github.com/gatk-workflows/gatk4-exome-analysis-pipeline

Let me know the tool which you want to use in gatk. Then I can give the command.

Badges
Science topic

More Bipin Raj Shekhar's questions See All

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Hello fellow researcher .. What is the meaning of your name?

I would like to create a small guide containing the meanings of the names .. Thanks to everyone who cooperates with me in achieving it.

03 March 2021 5,266 4 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

Is it possible to do piezoelectric coupling in ANSYS-APDL or COMSOL between tapered substrate and rectangular piezoelectric patch?

How to do Piezoelectric coupling in ANSYS-APDL or COMSOL between tapered substrate and rectangular piezoelectric patch? Piezoelectric coupling between the rectangular substrate and rectangular...

02 March 2021 9,833 3 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Adherance of Polyaniline coating over stainless steel?

Is the electropolymerisation of polyaniline coating over stainless steel (SS) via Cyclic voltammetry technique is really adherant? Else how to improve the adhesion of the coating, whether any...

01 March 2021 8,220 2 View

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

No title

Does anyone have the experience of using Taq Man probes in the QIAGEN Rotar- Gene qPCR machine?

01 March 2021 5,311 1 View

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

How to model the battery pack in PSIM or PSCAD?

Hello, I have simulated a single battery cell using Thevenin equivalent circuit. For a battery pack, I have a large number of cells connected in series and parallel connections. Is there any way...

28 February 2021 2,116 1 View

If I use REVEL score as a meta-predictor for clinical variant classification, what would be a reasonable cut-off to filter disease variants?

Ioannidis et al., 2019, reported the development of the REVEL score (rare exome variant ensemble learner) for redefining pathogenic variant classification, and Tian et al., 2019, reported that...

29 March 2020 2,450 2 View

What is the minimum and maximum cDNA input from FFPE samples in library preparation phase to perform the RNA SEQ by Ion Proton?

Dear All, 1 ug of permissible quality FFPE RNA is transcribed to cDNA through SSIV VILO RT kit. I have Qubit v.4 device, which can measure cDNA to a good extent. The cDNA ranges from 25-100 ng /...

11 November 2019 2,009 1 View

Which variant caller suggested for beginner of exome sequencing?

I am still new in bioinformatics field and now I am having an internship in MGI. Recently, we are given 2 sets of exome data which are diabetes type1 and diabetes type2. We already did with...

10 November 2019 2,226 2 View

Which approach is better and cost effective for detecting mutations in atp1a3 gene? Using mRNA and cDNA or Whole Exome Sequencing?

Hi. I am planning a screening study for apt1a3 gene in a family with clinical manifestations. The protein is about 1013 amino acids long, so its coding part is 3042 nucleotides. Numerous mutations...

09 October 2019 4,029 3 View

Which approach is better and cost effective for detecting mutations in atp1a3 gene? Using mRNA and cDNA or Whole Exome Sequencing?

Hi. I am planning a screening study for apt1a3 gene in a family with clinical manifestations. The protein is about 1013 amino acids long, so its coding part is 3042 nucleotides. Numerous mutations...

06 October 2019 7,655 6 View

How much primer designing differs from probe designing for exome sequencing? What if we design biotynylated primer instead of probe for capturing?

What are the criteria for designing biotinylated probes differ from primer designing?

24 September 2019 8,205 2 View

Anybody here who knows tool for custom designing of probe(target enrichment)?

Hi i want to capture 31Mb region in wheat for next generation sequencing. I asked for companies like Agilent and Nimblegen, but they are very costly. Therefore, does anybody know any tool like...

08 September 2019 6,520 0 View

How much primer designing differs from probe designing for exome sequencing? What if we design biotynylated primer instead of probe for capturing?

What are the criteria for designing biotinylated probes differ from primer designing?

08 September 2019 9,873 2 View

How to validate off-target effect and/or multiple mutations in a CRISPR-KO cell line?

I received a review comment, 'how I can validate that the phenotype I observed is not due to multiple mutations (or possibly, off-target effect) in a CRISPR-KO cell line' We performed several...

06 July 2019 8,673 1 View

What is/are the best free database to deposit new genetic variants with clinical significance?

Preferably, some database that does not take long to respond and whose input is not so complicated. Thanks in advance!

10 May 2019 1,559 2 View