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Pipeline publication

[…] iched samples were sequenced using 2 (2×100bp) lanes on an Illumina HiSeq 2000 (Illumina, Inc, San Diego, CA). Exome sequencing was performed in 9 individuals from Family 1: II1, II2, II3, II5, II7, III1, III2, III9 and III10. We screened for ETV6 mutations in the European families by Sanger sequencing of promoter regions, exons and exon flanking regions of ETV6., Reads passing Illumina chastity filter were subjected to a quality filter step that removed low quality bases from the 3′ end and retained pairs of reads if the trimmed reads for both members of the pair were 50 bp or longer. Paired reads that passed the quality filter were mapped to the reference human genome sequence (hg19) with GSNAP (Genomic Short-read Nucleotide Alignment Program, version 2012-07-20). Sequence calls for single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were performed using the GATK (Broad's Genome Analysis Toolkit, v2.1-8-g5efb575). , The program ANNOVAR (Annotate Variation, version 2012-03-08) was used to classify variants and to cross-reference all variants across various genetic variation databases. Included in ANNOVAR are databases to determine nonsynonymous and splice site variants (refGene.txt), variants in conserved genomic regions (phastConsElements46way.txt), variants in segmental duplications (genomicSuperDups.txt), and variant frequencies from 1000 genomes database (hg19_ALL.sites.2012_02.txt). Variants located outside of conserved regions, or with frequencies >1% were excluded from further analysis._ENREF_2 Only non-synonymous changes (SNPs and indels), splice site variants, and/or an aberrant stop codon changes were considered for further analysis. All insertion and deletion variants were considered damaging, whereas SNP variants were cross-referenced to the dbNSFP (database for nonsyn […]

Pipeline specifications

Software tools GSNAP, GATK, ANNOVAR
Diseases Anemia, Blood Platelet Disorders, Leukemia, Bone Marrow Diseases, Blood Platelet Disorders, Leukemia, Lymphoproliferative Disorders
Chemicals Nucleotides