*AICS5 PXN-EGFP cl50 AICS5 cl50 bam Track Settings
 
AICS5 cl50 alignment

Track collection: *AICS5 PXN-EGFP cl50

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Source data version: April 2018
Assembly: Human Dec. 2013 (GRCh38/hg38)

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).