Index of /public/dataset/HG002_SV_and_SNV_CCS
Name Last modified Size Description
Parent Directory -
consensusalignments/ 2019-03-04 15:28 -
consensusreads/ 2019-03-04 15:28 -
gatkhc/ 2019-03-04 13:52 -
pbsv/ 2019-03-10 20:44 -
subreads/ 2019-03-04 15:36 -
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