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| | README for 1000 Genomes Phase 1 short indels: |
| | Accurately calling short insertions and deletions from low coverage |
| | sequencing data has proven unexpectedly challenging. The present |
| | data set has gone through many twists and turns, and it is necessary |
| | to give some complex details in order to identify exactly which version |
| | is being deposited in dbSNP. The 1000 Genomes Project's goal has |
| | been to identify 95 % of all polymorphic sites above 0.5 % minor |
| | allele frequency, with a false positive rate per site not exceeding 5 %. |
| | Experimental validation of short indel polymorphism is challenging as |
| | well. The current set does not reach 95 % sensitivity, and it may or |
| | may not achieve a 5 % false positive rate (specificity). |
| | The Phase 1 integrated genotype release contains SNPs from both |
| | low coverage and exome capture sequencing, but its short indels |
| | come only from low coverage sequencing. These are merged from |
| | sets made by five different methods: freeBayes (Boston College), |
| | GATK (Broad Institute), Dindel (Sanger), Platypus (Oxford) and |
| | samtools (Sanger), using the 1000 Genomes Phase 1 low coverage |
| | sequence data for 1092 individuals. The merged indel calls were |
| | filtered using GATK Variant Quality Score Recalibration and |
| | restricted to bi-allelic sites only. These are found in directory |
| | ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp |
| | /release/20110521/supporting |
| | Further filtering beyond the restriction to biallelic indels is described |
| | by Hyun Min Kang as follows: |
| | 1. Exclusion of excessive 1-bp outliers |
| | We identified that a subset of indels from the low-coverage data have |
| | very high false positive rates. In particular, the following 10 samples |
| | showed excessive number of singleton indels (~1,000 to 23,000) that |
| | are mostly 1bp insertions. |
| | NA12144 |
| | NA20752 |
| | NA18626 |
| | NA19437 |
| | NA19439 |
| | NA19436 |
| | NA19448 |
| | NA18627 |
| | NA19313 |
| | NA19446 |
| | Upon further investigation, we found that the excessive 1bp singleton |
| | insertions are due to technical artifacts introduced in the sequencing |
| | step. We removed 162,928 1bp singleton insertions specific only to |
| | the 10 outlier samples. |
| | 2. In addition, we found much higher fraction of frameshift indels in |
| | low-coverage specific indels compared to the indels shared between |
| | low-coverage and exome data, suggesting that low-coverage specific |
| | coding indels may have enriched false positive rates. We removed |
| | additional 3,014 protein-coding frameshift indels exclusive to low- |
| | coverage samples to increase the specificity of the protein-coding |
| | indels. |
| | 3. Preliminary evaluations of INDEL call sets demonstrated high apparent |
| | false positive rate after the above steps, and rare INDELs demonstrated |
| | higher discordance with independent datasets. To extract high quality |
| | INDELs, we restricted the minimum allele frequency (before integration) |
| | to 0.5%, and additionally applied SVM approach to further filter out |
| | potential false positive INDELs guided by the indel genotypes from the |
| | Affymetrix Axiom genotyping chip were provided (Jeannette Schmidt & |
| | Jeremy Gollub). The SVM was trained using multiple features including |
| | (a) allele balance (b) inbreeding coefficient (c) flanking sequence complexity |
| | (d) homopolymer runs (e) strand bias (f) cycle bias (g) mapping quality |
| | (h) number of supporting non-ref reads, and (i) distance to nearby INDELs. |
| | A list of these excluded sites can be found in directory |
| | ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp |
| | /technical/working/20120131_indel_sites_to_exclude |
| | The Affymetrix indel genotypes are in directory |
| | ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp |
| | /technical/working/20120208_axiom_genotypes |
| | The final release set is currently in directory |
| | ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp |
| | /technical/working/20120312_phase1_v2_indel_cleaned_sites_list |
| | Full details of the underlying sequence data are given in files: |
| | ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp |
| | /sequence_indices/20101123.sequence.index |
| | /phase1/phase1.alignment.index |
| | All sequence coordinates are stated relative to the GRCh37 human |
| | genome reference sequence. |
