Germline SNP and you can Indel variant getting in touch with try performed following Genome Data Toolkit (GATK, v4.1.0.0) top behavior pointers 60 . Brutal reads were mapped to your UCSC peoples resource genome hg38 having fun with a good Burrows-Wheeler Aligner (BWA-MEM, v0.eight.17) 61 . Optical and you will PCR backup establishing and sorting is over playing with Picard (v4.step 1.0.0) ( Ft high quality get recalibration try completed with the newest GATK BaseRecalibrator ensuing when you look at the a final BAM apply for for each and every test. The resource files used for ft top quality rating recalibration was dbSNP138, Mills and you will 1000 genome gold standard indels and you may 1000 genome phase 1, provided throughout the GATK Money Bundle (last changed 8/).
Once studies pre-control, version calling was completed with this new Haplotype Caller (v4.step one.0.0) 62 from the ERC GVCF means to generate an intermediate gVCF apply for for each attempt, which were upcoming consolidated with the GenomicsDBImport ( equipment to produce just one apply for joint calling. Read more
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