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Method Detail
Submitter Method Handle: PADH-LAB_SPU
Submitter Method ID: ILUMINAHISEQ2000(TRUSEQ)
Submitted method description:
The genomic DNA was extracted using phenol-chloroform method [J. Sambrook, E. F. Fritsch, and T. Maniatis, ?Molecular cloning: A laboratory manual,? New York: Cold Spring Harbor Laboratory Press, 1989] from 5 ml of peripheral blood. After isolation, the D
h Sensitivity DNA Chip (Agilent, USA). The resulting library obtained was sequenced using an Illumina flow cell, and 202 cycles on the Illumina HiSeq 2000 platform (Illumina, USA).
The raw read sequences were filtered using following criteria: We used the NGS QC toolkit v2.2.1 to filter the raw reads for high-quality (cutoff read length for HQ = 70%, cutoff quality score = 20). The duplicated reads were removed with the MarkDuplicat
The paired-end sequence reads were aligned to human reference genomes with the BWA ver. 0.7.5a (default parameter except for -M; Mark shorter split hits as secondary). Aligned reads were realigned at indel positions with the GATK v2.3.9. The SNVs and Inde

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
PADH-LAB_SPU Assay WholeGenomeSequencing_SNP_Discovery 142