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Whole Genome Sequencing data analysis

aneekaneek Hyderabad, IndiaMember ✭✭
edited May 2017 in Ask the GATK team

We are new in whole genome sequencing (WGS) data analysis. Earlier received lots of help and suggestions from GATK team regarding whole exome sequencing analysis and in-house database generation. Recently we are into WGS anaysis and received few raw data from vendor. The Illumina paired end raw data (2 x 150 bp with 30X coverage) was received in parts from 8 lanes (fastq files). I have used FastQC for initial quality checking and have found that in some of the samples the reverse sequences (R2) failed to pass the quality especially at the end. I have attached some of those sample-wise failed fastqc reports here, if you can suggest about the quality of the data and also whether can be used for further analysis using GATK best practices guidelines for SNP & Indel discovery.

Thank you.

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by Sheila

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