Utility to genotype allelic variants of ApoE protein(e1,e2,e3,e4) using two SNPs rs429358 and rs7412 from a phased or unphased VCF.
| rs429358 | rs7412 | ApoE |
|---|---|---|
| C | T | ε1 |
| T | T | ε2 |
| T | C | ε3 |
| C | C | ε4 |
Requirements: python 3, pyvcf (available on PyPi (https://pypi.org/project/PyVCF/)
For the most accurate genotyping of all the APOE genotypes, the VCF should be phased (eg: eagle or SHAPEI2). This will help distinquish between the ambigous genotypes(e2e4 and e1e3). Without phasing, the e1e3 will default to the more probable e2e4 as e1 is very rare.
apoe-genotyper.py -v VCF -g [GRCh37,GRCh38] -o OUT [-p PROJECT] [-h]
| Args | Description |
|---|---|
| -v --vcf | VCF with APOE snps rs429358 and rs7412" (required) |
| -g --genome ["GRCh37","GRCh38"] | GRCh37 or GRCh38 reference genome" (required) |
| -o --out | APOE output file prefix (required) |
| -p --project | Project name (replaces VCF filename in output) |
| -h --help | Help |
Two output files are generated:
[output_prefix].tsv This file contains each sample's genotypes in a tab delimited file. Missing is specified with "."
| Column | Heading |
|---|---|
| Column 1 | project |
| Column 2 | sample |
| Column 3 | rs429358_T_C |
| Column 4 | rs7412_C_T |
| Column 5 | APOE |
| Column 6 | e1_dose |
| Column 7 | e2_dose |
| Column 8 | e3_dose |
| Column 9 | e4_dose |
[output_prefix].summary.tsv contains tab delimited list of summary information
| Column | Description |
|---|---|
| project | Project or VCF name |
| NSamples | Number of Samples |
| APOE_MISS_N | Samples missing APOE |
| APOE_MISS | Samples Missing APOE Frequency |
| ApoE1_N | Number of alleles with ApoE-1 (very rare) |
| ApoE1_pct | Per Cent of alleles with APOE-1 |
| ApoE2_N | Number of alleles with ApoE-2 |
| ApoE2_pct | Per Cent of alleles with APOE-1 |
| ApoE3_N | Number of alleles with ApoE-3 |
| ApoE3_pct | Per Cent of alleles with APOE-1 |
| ApoE4_N | Number of alleles with ApoE-4 |
| ApoE4_pct | Per Cent of alleles with APOE-1 |
| eMISSING_n | Number of samples with ApoE Missing Genotype |
| eMISSING_freq | Frequency of samples with ApoE Missing Genotype |
| e11_n | Number of samples with ApoE Genotype ε1ε1 |
| e11_freq | Frequency of ε1ε1 |
| e12_n | Number of samples with ApoE Genotype ε1ε2 |
| e12_freq | Frequency of ε1ε2 |
| e13_n | Number of samples with ApoE Genotype ε1ε3 |
| e13_freq | Frequency of ε1ε3 |
| e14_n | Number of samples with ApoE Genotype ε1ε4 |
| e14_freq | Frequency of ε1ε4 |
| e22_n | Number of samples with ApoE Genotype ε2ε2 |
| e22_freq | Frequency of ε2ε2 |
| e23_n | Number of samples with ApoE Genotype ε2ε3 |
| e23_freq | Frequency of ε2ε3 |
| e24_n | Number of samples with ApoE Genotype ε2ε4 |
| e24_freq | Frequency of ε2ε4 |
| e33_n | Number of samples with ApoE Genotype ε3ε3 |
| e33_freq | Frequency of ε3ε3 |
| e34_n | Number of samples with ApoE Genotype ε3ε4 |
| e34_freq | Frequency of ε3ε4 |
| e44_n | Number of Samples with ApoE Genotype ε4ε4 |
| e44_freq | Frequency of ε4ε4 |
| rs429358_R2 | rs429358_R2 (If Available from Imputed VCF) |
| rs7412_R2 | rs7412_R2 (If Available from Imputed VCF) |
#Examples python apoe-genotyper --project ADSP --vcf adsp_5k_phased.vcf.gz --out adsp_apoe_5k -g GRCh38 >adsp_apoe_5k.log
Will produce two files: adsp_apoe_5k.tsv adsp_apoe_5k.summary.tsv adsp_apoe_5k.log