Variant Calling using BCFTOOLS | BCFTOOLS Tutorial | Germline variant calling скачать в хорошем качестве

Variant Calling using BCFTOOLS | BCFTOOLS Tutorial | Germline variant calling

This tutorial shows you how to call variants in sequence data using bcftools Download the Ebook and script from here:   / variant-calling-77625038   *Thank me with a Coffee*: https://www.buymeacoffee.com/informat... *Tip me on Paypal*: https://www.paypal.com/paypalme/thein... *One-on-One coaching*: https://calendly.com/bioinformaticscoach *Consultation: https://calendly.com/bioinformaticscoach Reach out bioinformaticscoach@gmail.com Support My Work   / bigdataanalytics   https://www.buymeacoffee.com/informat... Subscribe to my channels Bioinformatics:    / @bioinformaticscoach   Data Science:    / @datasciencecoach   Short Clips:    / @bioinformaticscforbeginners   Reach out bioinformaticscoach@gmail.com source of data https://www.ncbi.nlm.nih.gov/pmc/arti... sra-database https://trace.ncbi.nlm.nih.gov/Traces... Input Files read 1 http://ftp.sra.ebi.ac.uk/vol1/run/ERR... read 2 http://ftp.sra.ebi.ac.uk/vol1/run/ERR... reference genome https://www.ncbi.nlm.nih.gov/nuccore/... accession id for reference genome CP000325.1 Documentation of the tools samtools http://www.htslib.org/doc/samtools-fl... bcftools http://samtools.github.io/bcftools/bc... https://samtools.github.io/bcftools/b... bwa http://bio-bwa.sourceforge.net/ sickle https://github.com/najoshi/sickle Setting up your PC How to install Anaconda Linux    • Install , Configure and Run Anaconda in  a...   MacOS    • How to Install and Run Anaconda in  MacOS ...   - GUI Installer    • Install, Configure and Run Anaconda in ANY...   - Command line installer How to install bcftools Compile the source code:    • How to install BCFTOOLS in any Linux Machi...   Using anaconda:   • Install BCFTOOLS in Linux using anaconda |...   Chapters 00:10 intro 01:35 install tools using conda 05:22 download sequence reads using wget 09:30 download the reference genome using your browser 11:04 download the reference genome using python 15:29 trim the raw reads using sickle 21:03 index the reference genome using bwa index command 24:11 genome mapping using bwa 26:53 convert the sam file to bam file using samtools 28:46 sort the bam file using samtools 29:42 map and sort using a one liner command 32:21 get the mapping statistics using samtools 35:33 get the converage information for bases and calculate genotype likelyhoods 39:18 call variants using bcftools 41:08 post-vcf analysis using bcftools #bioinformatics #genome #genomics #linuxforbeginners #genomesequencing Commands used in this tutorial bwa index bwa mem samtools view samtools sort samtools index samtools flagstat bcftools mpileup bcftools call bcftools view #bioinformaticsforbeginners #bioinformatics #bioinformática #linuxforbeginners #linux