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Method Detail
Submitter Method Handle: 1000GENOMES
Submitted method description:
The 1000 Genomes Pilot 2 SNP calls are based on deep coverage
whole genome DNA sequence data collected in 2008 using high
throughput sequencing on two family trios in the CEPH Utah and
HapMap sample collections. The DNA for each individual comes
from lymphoblastoid cell lines distributed by Coriell Institute,
Camden, NJ.
Average fold coverage by sequencing technology:
Illumina AB SOLiD LS 454
(CEU family # 1463)
NA12892 (mother) 26.7 x
NA12891 (father) 32.4 x
NA12878 (daughter) 33.2 x 16.6 x 13.5 x
(YRI family # Y117)
NA19238 (mother) 21.8 x
NA19239 (father) 26.4 x
NA19240 (daughter) 34.7 x 24.9 x 5.6 x
All sequence reads are mapped against the NCBI build 36.3 human
genome reference sequence of March, 2006. The pseudo-autosomal
regions on the Y chromosome are replaced with Ns for males; the
Y chromosome is omitted for females. Read mapping uses MAQ for
Illumina data, Corona_lite 4.01 for AB SOLiD data and SSAHA2 for
LS 454 data. Illumina read lengths are mostly 35 bp or 51 bp;
SOLiD reads are either 25 or 35 bp. In Illumina and LS 454 data,
PCR duplicates are removed using Picard MarkDuplicates and base
call quality values are recalibrated using GATK. For AB SOLiD
data, no duplicate removal or recalibration are done. Both
mapped and unmapped sequence reads are freely available in the
1000 Genomes ftp archive. All SNP locations in this submission
are stated relative to the NCBI version 36 human genome assembly.
DbSNP may subsequently update these coordinates to a later assembly.
The SNP and genotype calls released for each trio in March 2010
are the intersection of results from two separate computational
analyses applied to the same mapped sequence reads in the .bam
files available from the 1000 Genomes ftp archive. Both analyses
are likelihood-based. They differ in some details of pre-processing
and modeling, and in the thresholds applied afterward to exclude
marginal sites.
At Broad Institute, a pre-processing step uses GATK to locally
realign all sequence reads which cover either an indel or a cluster
of apparent polymorphisms. The likelihood based SNP calling treats
each trio as three unrelated females. The criterion to include
a potential polymorphic site in the set of final Broad calls is:
Consistent with Mendelian inheritance AND
SNP call quality score (QUAL) >= 50, AND
Allele balance (AB) <= 75% reference, AND
Depth of coverage (DP) <= 360, AND
Strand bias (SB) <= -0.10, AND
(Number of covering reads with mapping quality score zero (MQ0)
<= 0.1 * depth of coverage OR (MQ0 < 4)).
At University of Michigan, local realignment evaluates SNP calls
after they are made. The likelihood procedure makes use of known
gender and family relationships. Genotypes are phased where possible
using transmission among family members, otherwise reported as
"unphased". A potential polymorphic site must satisfy:
(a) For some sequencing technology, the depth of coverage combined
across all trio members at this site is between 50% and 150%
of the average depth, and the root mean squared (RMS) mapping
quality score of covering reads is at least 30.
(b) Sequence data passing (a) is present for each person in the trio
(although perhaps not from the same sequencing technology).
(c) The posterior probability for at least one non-reference
allele exceeds 0.999 (SNP call quality score > 30).
(d) Away from a potential indel detected by local realignment.
The current release set consists of all sites which are called by
both analyses, including passing the criteria shown above.
Data availability:
All of the mapped and unmapped original sequence reads are publicly
available from the 1000 Genomes anonymous ftp archive. They are
indexed in file
and available in subdirectories called "pilot_data/data/NA*/sequence_read"
(where "NA*" is replaced by one of the HapMap NA identifiers). VCF format
SNP calls and genotype calls are currently available in subdirectories of
although this may not be a permanent location.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
1000GENOMES Assay pilot_2_CEU_trio_final_release 132
1000GENOMES Assay pilot_2_YRI_trio_final_release 132