AICS58 CTNNB1-mEGFP cl67 AICS58 cl67 var Track Settings
 
AICS58 cl67 variants

Track collection: AICS58 CTNNB1-mEGFP cl67

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Filters

Exclude variants with Quality/confidence score (QUAL) score less than
Exclude variants with these FILTER values:
 
LowQual (Low quality)
indel_FS200.0 (FS > 200.0)
indel_QD2.0 (QD < 2.0)
indel_ReadPosRankSum-20.0 (ReadPosRankSum < -20.0)
indel_SOR10.0 (SOR > 10.0)
snp_FS60.0 (FS > 60.0)
snp_MQ40.0 (MQ < 40.0)
snp_MQRankSum-12.5 (MQRankSum < -12.5)
snp_QD2.0 (QD < 2.0)
snp_ReadPosRankSum-8.0 (ReadPosRankSum < -8.0)
snp_ReadPosRankSum3.0 (SOR > 3.0)
Minimum minor allele frequency (if INFO column includes AF or AC+AN):


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Data schema/format description and download
Source data version: July 2019
Assembly: Human Dec. 2013 (GRCh38/hg38)

AICS58 CTNNB1-mEGFP

Description

This track hub contains the whole exome sequences and variant calls for AICS58 CTNNB1-mEGFP clone 67 (public clone).

AICS58 CTNNB1-mEGFP

AICS58 CTNNB1-mEGFP is part of the Allen Cell Collection of fluorescently tagged hiPSC lines created by the Allen Institute for Cell Science. Clone 67 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 using the Broad Institute's Genomic Services. Exome capture was carried out using Illumina's Nextera Rapid Capture Exome Kit, and 76bp paired-end reads were generated on an Illumina HiSeq 4000.

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).