NGS Data Processing
Whole Genome/Exome sequencing data processing
-Required Computing Skills
-Raw Genomic/Exomic data quality control and manipulation: Fastx toolkit…
-Genomic/Exomic Mapping: BWA, Bowtie, MAQ, SOAP3…(Mapping raw data from; 454, SOLiD, Illumina, Ion torrent etc.)
-Data manipulations (for SAM/BAM files): Pysam, Picard…
-Filtering, Sorting, Indexing,visualizing and variant calling (for SAM/BAM files): Samtools, GATK, IGV…
-Filtering and recalibrating variants (for BCF/VCF files)
-Variant annotation: SNPeff, ANNOVAR, SeattleSeq…
-Validating, merging, comparing and calculating VCF files: VCFtools
-Viewing, sorting and filtering variants: Varsifter
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