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dbSNP

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Method Detail
Submitter Method Handle: TOPMED
Submitter Method ID: FREEZE 5
Submitted method description:
38x average coverage deep whole genome sequencing of over 60,000 individuals,
followed by variant discovery, genotyping and site-level filtering for SNPs
and short indels. This uses the current 'vt' implementation of likelihood-based
variant calling. All sequencing is done from blood DNA, not lymphoblastoid
cell lines (with the exception of NA12878 and NA19238 control samples) and
uses PCR-free library preps (except for < 500 legacy samples sequenced prior
to initiating the project). Sequence data and further description of methods
are available from dbGaP studies with 'TOPMed' in the study name.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
TOPMED Assay Freeze 5 variant calls-chr1 150
TOPMED Assay Freeze 5 variant calls-chr10 150
TOPMED Assay Freeze 5 variant calls-chr11 150
TOPMED Assay Freeze 5 variant calls-chr12 150
TOPMED Assay Freeze 5 variant calls-chr13 150
TOPMED Assay Freeze 5 variant calls-chr14 150
TOPMED Assay Freeze 5 variant calls-chr15 150
TOPMED Assay Freeze 5 variant calls-chr16 150
TOPMED Assay Freeze 5 variant calls-chr17 150
TOPMED Assay Freeze 5 variant calls-chr18 150
TOPMED Assay Freeze 5 variant calls-chr19 150
TOPMED Assay Freeze 5 variant calls-chr2 150
TOPMED Assay Freeze 5 variant calls-chr20 150
TOPMED Assay Freeze 5 variant calls-chr21 150
TOPMED Assay Freeze 5 variant calls-chr22 150
TOPMED Assay Freeze 5 variant calls-chr3 150
TOPMED Assay Freeze 5 variant calls-chr4 150
TOPMED Assay Freeze 5 variant calls-chr5 150
TOPMED Assay Freeze 5 variant calls-chr6 150
TOPMED Assay Freeze 5 variant calls-chr7 150
TOPMED Assay Freeze 5 variant calls-chr8 150
TOPMED Assay Freeze 5 variant calls-chr9 150
TOPMED Assay Freeze 5 variant calls-chrX 150