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Whole Genome Variant Calling @ Linux
Rating: 3.9 out of 5(25 ratings)
138 students

Whole Genome Variant Calling @ Linux

GATK4 variant calling pipeline
Created byDr. Rashid Saif
Last updated 8/2020
Urdu

What you'll learn

  • GATK4 variant calling pipeline

Course content

1 section13 lectures6h 3m total length
  • Linux Overview- Concept of Root & Home (Part_1)31:13
  • Linux Overview- Concept of ls, cat, cp, mv & rm commands (Part_2)22:36
  • Linux GATK4- Uploading Input files (Step 1)22:31
  • Linux GATK4- Concatenating datasets & trimming with fastp (Step 2)29:38
  • Linux GATK4- Quality checks with MultiQC (Step 3)28:10
  • Linux GATK4- Mapping with BWA-MEM (Step 4)22:55
  • Linux GATK4- Converting SAM file to BAM with Samtools (Step 5)22:02
  • Linux GATK4- Mapping of Glasgow & Wuhan strains using bowtie2 (Step 6)25:09
  • Linux GATK4- AddReplaceReadGroup, Sorting & MarkDuplicates with Picard (Step 7)41:52
  • Linux GATK4- Variant Calling with Mutect2 (Step 8)37:19
  • Linux GATK4 - VcfAllelicPrimitives with Vcflib (Step 9)18:57
  • Linux GATK4- Annotating Vcf files with SnpEff (Step 10)39:38
  • Linux GATK4- ExtractFields with SnpSift (Step 11)21:55

Requirements

  • Basics knowledge of command line interface, genomics and sequencing technologies

Description

This course will untangle the mysteries of students stand alone on the boundaries of molecular genetics and bioinformatics, they will come to know that why life sciences researchers are direly needed computation skills, on which type of biological data computation will apply, how Linux operating system compute multi-omics problems, and how the fields of bioinformatics and computational biology are evolving to circumvent modern biology problems.

In the time to come, biologists will not restrain to the wet-labs only, so let's come and modify yourselves with bioinformatics data science tools for analysis, visualization and inferring crux of your big genomic datasets. This course is the right stop, that will help you to overwhelm your transition from wet to dry-labs and facilitate you to analyze the whole genome NGS data for variant calling... that speaks loud around.

Other courses of the same author are also available on molecular docking using MOE, whole-genome variant calling using Galaxy, differential gene expression analysis using RNA-Seq, and genomic selection signature pipelines using pooled-heterozygosity statistics on NGS pooled-seq datasets.

For further readings, you may visit the author's google scholar page for different bioinformatics data analysis pipelines with their application in human, animal, and microbial studies.

"Decode Genomics" webpage may also be explored for hands-on training in molecular diagnostics for local students/enthusiasts and interactive online courses in NGS data analysis may also be scheduled.

Who this course is for:

  • University student in the field of Biotechnology, Microbiology, Genetics, Bioinformatics and other related disciplines in life sciences