Index of /public/dataset/HG002_SV_and_SNV_CCS

Icon  Name                    Last modified      Size  Description
[PARENTDIR] Parent Directory - [DIR] gatkhc/ 2019-03-04 13:52 - [DIR] consensusalignments/ 2019-03-04 15:28 - [DIR] consensusreads/ 2019-03-04 15:28 - [DIR] subreads/ 2019-03-04 15:36 - [DIR] pbsv/ 2019-03-10 20:44 - [TXT] README.txt 2019-03-10 20:48 1.6K
SAMPLE
    HG002 extracted DNA

METHODS
    Shearing          15 kb with Megaruptor
    Library prep      TPK 1.0
    Size selection    Fraction 4 (11 kb) with Sage ELF
    Sequencing        Sequel System II with "Early Access" binding kit (101-490-800) and chemistry (101-490-900)
    Run time          12 hour pre-extension; 30 hour movie
    CCS               SMRT Link 6.1 "Early Access" Circular Consensus Sequence Analysis (ccs v3.2.1)
    Reference         hs37d5 (GRCh37 with decoy)
    Alignment         pbmm2 --preset CCS
    Variant Calling   GATK v4.0.10.1 HaplotypeCaller
    SV Calling        SMRT Link Structural Variant Calling (powered by pbsv)
    Variant Phasing   WhatsHap v0.17

DOWNLOAD
    MD5 checksums are listed in MD5.txt

FOLDERS
    subreads                                  Basecalled reads and metadata for three Sequel II SMRTCells 8M loaded with 11kb HG002 libraries
    consensusreads                            Circular Consensus reads and metadata for runs above
    consensusalignments					      CCS reads above, aligned to hs37d5 with pbmm2.
    gatk4hc                                   Small variants called with GATK4 HaplotypeCaller and phased with WhatsHap
        /GIAB_small_variant_v3.3.2_benchmark  Benchmarked against GIAB small variant v3.3.2 with hap.py
        /GIAB_phasing_benchmark               Benchmarked against 10X/Trio phased variant set.
    pbsv                                      Structural variants called with SMRT Link Structural Variant Calling (powered by pbsv)
        /truvari-giab-v0.6                    Benchmarked against GIAB structural variant v0.6 with Truvari