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

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

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