bolekj/Plasmodium_falciparum

Reproducing methods from "Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia" Repo contains scripts, results, and report. # Plasmodium_falciparum Reproducing methods from "Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia" Repo contains scripts, results, and report. ### Downloading raw data ```` $ wget ftp://ngs.sanger.ac.uk ```` ## Creating index files ### 1.For reference genome ```` $gatk CreateSequenceDictionary -R Pfalciparum.genome.fasta $samtools faidx Pfalciparum.genome.fasta ```` ### 2.For bam files (samples) ```` #indexing of bam files for file in *bam; do samtools index -b $file done ```` ## HaplotypeCalling ```` #variant calling gatk --java-options "-Xmx4g" HaplotypeCaller \ -R Pfalciparum.genome.fasta \ -I PA0007-C.bam \ -O v7.g.vcf.gz \ -ERC GVCF ```` ### Combining vcf samples ```` #combining the variants gatk CombineGVCFs \ -R Pfalciparum.genome.fasta \ --variant v7.g.vcf.gz \ --variant v8.g.vcf.gz \ -O combined.g.vcf.gz ```` ### Genotyping ```` #genotyping variants gatk --java-options "-Xmx96g -Xms96g" GenotypeGVCFs \ -R Pfalciparum.genome.fasta \ -V combined.g.vcf.gz \ -O genotyped.vcf.gz ```` ## Hard filtering ### variant to table ```` gatk VariantsToTable -V genotyped.vcf -F QD -F FS -F SOR -F MQ -F DP -O QD.table ```` ### visulisition of tables in R. ```` library(ggplot2) QD.plot 5.0" \ --filter-name "MQ32"\ --filter-expression "MQ 5.0" \ --filter-name "MQ32"\ --filter-expression "MQ Pf.ann.vcf ```` ### For snps ```` java -Xmx8g -jar snpEff.jar GRCh37.75 /opt/data/bole/variant/SNPfiltered.vcf.gz > snp.ann.vcf ```` ## Running loop(working) ``` parallel 'gatk HaplotypeCaller -R Pfalciparum.genome.fasta -I {} -O {}.hppc.g.vcf' ::: *.bam ```` ## challenge ### 1.viewing from HPC using IGV. ## NEXT STEP * Automate using workflow.