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| # pylae | ||
| Local ancestry estimation | ||
| Python for local ancestry estimation | ||
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| ### Data preparation stage: | ||
| (will be performed by script itself in future) | ||
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| 1. In case we have .bed .bim .fam files, we need to convert to vcf using plink: | ||
| ```bash | ||
| plink2 --bfile <bfile_prefix> --recode vcf --out <vcf_file> | ||
| ``` | ||
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| 2. Calculate snp frequencies for population groups using bcftools. | ||
| User groups defined in file `configs/vcf_groups.txt`: | ||
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| ```bash | ||
| cat <vcf_file> | bcftools view -c 1 -Ou | bcftools +fill-tags -Ou -- -S configs/vcf_groups.txt -t AF | bcftools query -H -f "%CHROM %POS %ID %AF_<group> %AF_Mediterranean %AF_NativeAmerican %AF_NorthEastAsian %AF_NorthernEuropean %AF_Oceanian %AF_SouthAfrican %AF_SouthEastAsian %AF_SouthWestAsian %AF_SubsaharanAfrican\n" > <group>.<sample>.txt | ||
| ``` | ||
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| In case vcf file is (b)gzipped use samtools tabix. | ||
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| 3. Then use main script. | ||
| Currently supported modes: bayes, fb. | ||
| Note: fb is around 20 times slower. | ||
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| ```bash | ||
| python3 src/process_individuals.py --mode fb --window-len 200 <group>.<sample>.txt | ||
| ``` | ||
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| Example pipeline: | ||
| ```bash | ||
| plink2 --bfile America.QuechuaCandelaria_3.txt_GENO --recode vcf --out America.QuechuaCandelaria_3_GENO | ||
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| cat America.QuechuaCandelaria_3_GENO.vcf | bcftools view -c 1 -Ou | bcftools +fill-tags -Ou -- -S vcf_groups.txt -t AF | bcftools query -H -f "%CHROM %POS %ID %AF_QuechuaCandelaria_3 %AF_Mediterranean %AF_NativeAmerican %AF_NorthEastAsian %AF_NorthernEuropean %AF_Oceanian %AF_SouthAfrican %AF_SouthEastAsian %AF_SouthWestAsian %AF_SubsaharanAfrican\n" > "QuechuaCandelaria_3.GA002786.txt" | ||
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| python3 src/process_individuals.py --mode fb --window-len 200 "QuechuaCandelaria_3.GA002786.txt" | ||
| ``` | ||
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| ## Estimated performance: | ||
| for vcf file with around 120k SNPs. | ||
| |mode|exec time, m| ? | | ||
| |--|--|--| | ||
| |fb | 20 | ? | | ||
| |bayes| 1 | ? | |
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| ;SouthWestAsian;NorthernEuropean;Mediterranean;SouthAfrican;SubsaharanAfrican;NativeAmerican;NorthEastAsian;Oceanian;SouthEastAsian | ||
| SouthWestAsian;0;0.03249898;0.03262916;0.08696902;0.08696902;0.07102692;0.06377022;0.08496066;0.07167506 | ||
| NorthernEuropean;0.03249898;0;0.00743894;0.083706606;0.083706606;0.067764506;0.060507806;0.081698246;0.068412646 | ||
| Mediterranean;0.03262916;0.00743894;0;0.08383678;0.08383678;0.06789468;0.06063798;0.08182842;0.06854282 | ||
| SouthAfrica;0.08696902;0.083706606;0.08383678;0;0.06;0.1131131;0.1058564;0.12704684;0.11376124 | ||
| SubsaharanAfrican;0.08696902;0.083706606;0.08383678;0.06;0;0.1131131;0.1058564;0.12704684;0.11376124 | ||
| NativeAmerican;0.07102692;0.067764506;0.06789468;0.1131131;0.1131131;0;0.0463173;0.09783194;0.08454634 | ||
| NorthEastAsian;0.06377022;0.060507806;0.06063798;0.1058564;0.1058564;0.0463173;0;0.09057524;0.07728964 | ||
| Oceanian;0.08496066;0.081698246;0.08182842;0.12704684;0.12704684;0.09783194;0.09057524;0;0.0895936 | ||
| SouthEastAsian;0.07167506;0.068412646;0.06854282;0.11376124;0.11376124;0.08454634;0.07728964;0.0895936;0 |
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| Mediterranean_Mediterranean1 Mediterranean | ||
| Mediterranean_Mediterranean2 Mediterranean | ||
| Mediterranean_Mediterranean3 Mediterranean | ||
| Mediterranean_Mediterranean4 Mediterranean | ||
| Mediterranean_Mediterranean5 Mediterranean | ||
| Mediterranean_Mediterranean6 Mediterranean | ||
| Mediterranean_Mediterranean7 Mediterranean | ||
| Mediterranean_Mediterranean8 Mediterranean | ||
| Mediterranean_Mediterranean9 Mediterranean | ||
| Mediterranean_Mediterranean10 Mediterranean | ||
| Mediterranean_Mediterranean11 Mediterranean | ||
| Mediterranean_Mediterranean12 Mediterranean | ||
| Mediterranean_Mediterranean13 Mediterranean | ||
| Mediterranean_Mediterranean14 Mediterranean | ||
| Mediterranean_Mediterranean15 Mediterranean | ||
| NativeAmerican_NativeAmerican1 NativeAmerican | ||
| NativeAmerican_NativeAmerican2 NativeAmerican | ||
| NativeAmerican_NativeAmerican3 NativeAmerican | ||
| NativeAmerican_NativeAmerican4 NativeAmerican | ||
| NativeAmerican_NativeAmerican5 NativeAmerican | ||
| NativeAmerican_NativeAmerican6 NativeAmerican | ||
| NativeAmerican_NativeAmerican7 NativeAmerican | ||
| NativeAmerican_NativeAmerican8 NativeAmerican | ||
| NativeAmerican_NativeAmerican9 NativeAmerican | ||
| NativeAmerican_NativeAmerican10 NativeAmerican | ||
| NativeAmerican_NativeAmerican11 NativeAmerican | ||
| NativeAmerican_NativeAmerican12 NativeAmerican | ||
| NativeAmerican_NativeAmerican13 NativeAmerican | ||
| NativeAmerican_NativeAmerican14 NativeAmerican | ||
| NativeAmerican_NativeAmerican15 NativeAmerican | ||
| NorthEastAsian_NorthEastAsian1 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian2 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian3 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian4 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian5 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian6 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian7 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian8 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian9 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian10 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian11 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian12 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian13 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian14 NorthEastAsian | ||
| NorthEastAsian_NorthEastAsian15 NorthEastAsian | ||
| NorthernEuropean_NorthernEuropean1 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean2 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean3 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean4 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean5 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean6 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean7 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean8 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean9 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean10 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean11 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean12 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean13 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean14 NorthernEuropean | ||
| NorthernEuropean_NorthernEuropean15 NorthernEuropean | ||
| Oceanian_Oceanian1 Oceanian | ||
| Oceanian_Oceanian2 Oceanian | ||
| Oceanian_Oceanian3 Oceanian | ||
| Oceanian_Oceanian4 Oceanian | ||
| Oceanian_Oceanian5 Oceanian | ||
| Oceanian_Oceanian6 Oceanian | ||
| Oceanian_Oceanian7 Oceanian | ||
| Oceanian_Oceanian8 Oceanian | ||
| Oceanian_Oceanian9 Oceanian | ||
| Oceanian_Oceanian10 Oceanian | ||
| Oceanian_Oceanian11 Oceanian | ||
| Oceanian_Oceanian12 Oceanian | ||
| Oceanian_Oceanian13 Oceanian | ||
| Oceanian_Oceanian14 Oceanian | ||
| Oceanian_Oceanian15 Oceanian | ||
| QuechuaCandelaria_3_GA002786 QuechuaCandelaria_3 | ||
| SouthAfrican_SouthAfrican1 SouthAfrican | ||
| SouthAfrican_SouthAfrican2 SouthAfrican | ||
| SouthAfrican_SouthAfrican3 SouthAfrican | ||
| SouthAfrican_SouthAfrican4 SouthAfrican | ||
| SouthAfrican_SouthAfrican5 SouthAfrican | ||
| SouthAfrican_SouthAfrican6 SouthAfrican | ||
| SouthAfrican_SouthAfrican7 SouthAfrican | ||
| SouthAfrican_SouthAfrican8 SouthAfrican | ||
| SouthAfrican_SouthAfrican9 SouthAfrican | ||
| SouthAfrican_SouthAfrican10 SouthAfrican | ||
| SouthAfrican_SouthAfrican11 SouthAfrican | ||
| SouthAfrican_SouthAfrican12 SouthAfrican | ||
| SouthAfrican_SouthAfrican13 SouthAfrican | ||
| SouthAfrican_SouthAfrican14 SouthAfrican | ||
| SouthAfrican_SouthAfrican15 SouthAfrican | ||
| SouthEastAsian_SouthEastAsian1 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian2 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian3 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian4 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian5 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian6 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian7 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian8 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian9 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian10 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian11 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian12 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian13 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian14 SouthEastAsian | ||
| SouthEastAsian_SouthEastAsian15 SouthEastAsian | ||
| SouthWestAsian_SouthWestAsian1 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian2 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian3 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian4 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian5 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian6 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian7 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian8 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian9 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian10 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian11 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian12 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian13 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian14 SouthWestAsian | ||
| SouthWestAsian_SouthWestAsian15 SouthWestAsian | ||
| SubsaharanAfrican_SubsaharanAfrican1 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican2 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican3 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican4 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican5 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican6 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican7 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican8 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican9 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican10 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican11 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican12 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican13 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican14 SubsaharanAfrican | ||
| SubsaharanAfrican_SubsaharanAfrican15 SubsaharanAfrican |
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