Index of /public/dataset/HiFiTE_SqIIe/Feb_2023/BRCA1_2

Icon  Name                                               Last modified      Size  Description
[PARENTDIR] Parent Directory                                                        -   
[TXT] README.txt                                         2023-02-24 11:48  1.2K  
[   ] HG002.GRCh38_noalt.deepvariant.haplotagged.bam.bai 2023-02-24 11:49  243K  
[   ] HG002.fastq.gz                                     2023-02-24 11:48  219M  
[   ] HG002.GRCh38_noalt.deepvariant.haplotagged.bam     2023-02-24 11:49  225M  
[   ] human_GRCh38_no_alt_analysis_set.fasta             2023-02-24 11:53  2.9G  

OVERVIEW
    PacBio HiFi reads for HG002 from target enrichment BRCA1 and BRCA2 panel.

METHODS
    SHEARING    Megaruptor v3, speed 43 to target size of 9kb.
    TWIST LIBRARY    Prepared according to https://www.twistbioscience.com/resources/protocol/long-read-library-preparation-and-standard-hyb-v2-enrichment
            Probes: Custom panel PacBio_BRCA1_BRCA2_v2_TE-92849752
    PACBIO LIBRARY     SMRTbell prep kit 3.0 Prepared according to https://www.pacb.com/wp-content/uploads/Procedure-checklist-Preparing-multiplexed-amplicon-libraries-using-SMRTbell-prep-kit-3.0.pdf
    SEQUENCING    Sequel IIe system, 24 hr movie
    ANALYSIS    Demultiplex with lima v2.5.0
            Mark PCR Duplicates with pbmarkdups v1.0.2
            Align to GRCh38_no_alt_analysis_set with pbmm2 v1.7.0
            Call variants with pbsv v2.8 and DeepVariant v1.4.0
            Phase with whatshap 1.1

FILE DESCRIPTION
HG002.GRCh38_noalt.deepvariant.haplotagged.bam            aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag)
HG002.fastq.gz                            demultiplexed HiFi reads
human_GRCh38_no_alt_analysis_set.fasta                reference used to generate BAM files