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Pipeline publication

[…] b' paired end reads on a HiSeq2000 platform subsequently (Illumina, San Diego, CA, USA). We independently performed high-throughput sequencing of each captured library to ensure that each sample met the desired average fold coverage. Coverage was calculated by counting the number of sequenced bases that mapped to the target regions. Bases mapping to regions within a 200-bp range of a target were considered \xe2\x80\x9cnear target\xe2\x80\x9d., Raw image files were processed using Illumina base-calling software 1.7 with default parameters, and the sequences for each individual were generated as 90-bp paired-end reads. After filtering, high-quality reads were aligned to the human genome (GRCH37, UCSC hg19) using the Burrows-Wheeler Aligner program []. SAMtools [] and SOAPsnp [] were used for the identification of small insertions or deletions (InDels) and single nucleotide polymorphisms (SNPs), respectively. SNPs were called using SOAPsnp with options:-r 0.00005-e 0.0001-t-u-L 90-Q L. Next, filters of quality score (\xe2\x89\xa520), neighbor distance (\xe2\x89\xa55) and depth (\xe2\x89\xa54) were applied to the SNPs calling results. Finally, ANNOVAR [] was used for the annotation of InDels and SNPs., Variants were selected for follow-up when all of the following criteria applied:, Variants were located in the exonic region or were within -2 bp away from an exon/intron boundary (splicing)., Variants were InDels, nonsynonymous (missense or nonsense) or splicing variants., Variants did not occur within the 1000 Genomes (1000G) data with a minor allele frequency (MAF) greater than 0.01[]., Variants were consistent with the known pattern of inheritance of the respective gene., If prioritization resulted in a single strong candidate allele (a nonsense or canonical splice site variant) in a recessively acting gene, a manual literature ' […]

Pipeline specifications

Software tools BWA, SAMtools, SOAPsnp, ANNOVAR
Organisms Homo sapiens
Diseases Breast Neoplasms, Breast Diseases, Anemia, Bone Marrow Diseases, Anemia, Hypoplastic, Congenital, DNA Repair-Deficiency Disorders, Neoplasms, Neoplastic Syndromes, Hereditary