AICS5 PXN-EGFP
Description
This track hub contains the whole exome sequences and variant calls for AICS5 PXN-EGFP clone 50 (public clone) and clone 52.
AICS5 PXN-EGFP
AICS5 PXN-EGFP is part of the Allen Cell Collection of fluorescently tagged hiPSC lines created by the Allen Institute for Cell Science. Clone 50 is publically available through Coriell. For more information on the tagged structure including live cell images visit the Allen Cell Collection, Cell Stories, and Allen Cell Explorer
Methods
Sequencing
Libraries were prepared and sequenced by Covance Genomics Services. Exome capture was carried out using a Nimblegen SeqCap EZ Exome Enrichment Kit v3.0, and 151bp paired-end reads were generated on an Illumina HiSeq 2500.
Analysis
Adapters were trimmed using cutadapt (version 1.13). Reads were aligned to GRCh38 using bwa mem (version 0.7.13). Duplicate reads were identified using MarkDuplicates from Picard (version 2.3.0). Local realignment around indels and base quality recalibration were performed using GATK (version 3.5). Variants were called using GATK's HaplotypeCaller and hard filtered (see variants track for filtering criteria).
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