Undergraduate research Adrian Salguero and Liam McKay under guidance by Russ Corbett-Detig PhD
- Takes a VCF (Variant Call Format) SNP data file (NGS read pileup data/genotype data/...)
- Converts it into a file (like example.panel) for input into russcd/Ancestry_HMM
| #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | NA06984 | NA06985 | NA06986 | NA06989 | NA06994 | NA07000 | NA07037 | NA07048 | NA07051 | NA07346 | NA07347 | NA07357 | NA10847 | NA10851 | NA11829 | NA11830 | NA11831 | NA11832 | NA11840 | NA11843 | NA11881 | NA11893 | NA11918 | NA11919 | NA11920 | NA11930 | NA11992 | NA11994 | NA11995 | NA12003 | NA12004 | NA12005 | NA12006 | NA12043 | NA12044 | NA12045 | NA12058 | NA12144 | NA12154 | NA12155 | NA12156 | NA12234 | NA12249 | NA12272 | NA12273 | NA12275 | NA12282 | NA12283 | NA12286 | NA12287 | NA12340 | NA12341 | NA12342 | NA12347 | NA12348 | NA12383 | NA12400 | NA12413 | NA12414 | NA12489 | NA12546 | NA12716 | NA12717 | NA12718 | NA12748 | NA12749 | NA12750 | NA12751 | NA12760 | NA12761 | NA12762 | NA12763 | NA12775 | NA12776 | NA12812 | NA12814 | NA12815 | NA12828 | NA12829 | NA12830 | NA12842 | NA12843 | NA12872 | NA12873 | NA12874 | NA12878 | NA12889 | NA12890 | NA12891 | NA12892 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1105366 | . | T | C | . | PASS | AA=T;AC=4;AN=114;DP=3251 | GT:DP | ./.:0 | ./.:0 | 0/0:107 | ./.:0 | ./.:0 | 0/0:25 | 0/0:30 | 0/0:31 | 0/0:57 | 0/0:69 | 0/0:53 | 0/0:225 | ./.:0 | 0/0:6 | 0/0:79 | ./.:0 | 0/0:110 | 0/0:79 | ./.:0 | ./.:0 | ./.:0 | 0/0:43 | 1/0:54 | 0/0:7 | 0/0:89 | 0/0:87 | 0/0:98 | 0/0:83 | ./.:0 | 0/0:62 | 0/0:1 | 0/0:4 | ./.:0 | 0/0:97 | ./.:0 | 0/0:115 | ./.:0 | 0/0:77 | 0/0:8 | 0/0:63 | ./.:0 | 0/0:92 | ./.:0 | 0/0:1 | 0/0:1 | ./.:0 | ./.:0 | ./.:0 | ./.:0 | 0/0:76 | ./.:0 | ./.:0 | ./.:0 | 0/0:41 | 0/0:35 | 1/0:135 | ./.:0 | 1/0:116 | 0/0:6 | ./.:0 | 0/0:147 | ./.:0 | ./.:0 | 0/0:4 | 0/0:40 | 1/0:23 | ./.:0 | 0/0:1 | 0/0:2 | ./.:0 | 0/0:7 | 0/0:1 | 0/0:90 | 0/0:49 | ./.:0 | 0/0:6 | ./.:0 | 0/0:82 | 0/0:31 | 0/0:7 | 0/0:9 | 0/0:7 | ./.:0 | ./.:0 | ./.:0 | 0/0:176 | 0/0:3 | 0/0:81 | 0/0:67 | 0/0:156 |
| 1 | 1105411 | . | G | A | . | PASS | AA=G;AC=1;AN=106;DP=2676 | GT:DP | ./.:0 | ./.:0 | 0/0:92 | ./.:0 | ./.:0 | 0/0:23 | 0/0:17 | 0/0:37 | 1/0:61 | 0/0:60 | 0/0:47 | 0/0:126 | ./.:0 | 0/0:5 | 0/0:79 | ./.:1 | 0/0:87 | 0/0:76 | ./.:0 | ./.:0 | ./.:0 | 0/0:26 | 0/0:50 | 0/0:3 | 0/0:92 | 0/0:79 | 0/0:93 | 0/0:73 | ./.:0 | 0/0:43 | 0/0:1 | 0/0:2 | ./.:0 | 0/0:53 | ./.:0 | 0/0:81 | ./.:0 | 0/0:67 | 0/0:5 | 0/0:58 | ./.:0 | 0/0:59 | ./.:0 | ./.:0 | ./.:0 | ./.:0 | ./.:0 | ./.:0 | ./.:0 | 0/0:58 | ./.:0 | ./.:0 | ./.:0 | 0/0:34 | 0/0:20 | 0/0:101 | ./.:0 | 0/0:107 | 0/0:7 | ./.:0 | 0/0:121 | ./.:0 | 0/0:1 | 0/0:1 | 0/0:31 | 0/0:28 | ./.:0 | ./.:0 | 0/0:2 | ./.:0 | 0/0:8 | ./.:0 | 0/0:59 | 0/0:49 | ./.:0 | 0/0:6 | ./.:0 | 0/0:51 | 0/0:29 | ./.:4 | 0/0:7 | 0/0:3 | ./.:0 | ./.:0 | ./.:0 | 0/0:168 | 0/0:4 | 0/0:84 | 0/0:47 | 0/0:150 |
Source: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/exon/snps/
Converted to:
| 1 | 20916748 | 1 | 0 | 0 | 4 | 0.20916748000000002 | 4 | 0 | 0 | 0 | 6 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 4 | 3 | 0 | 0 | 0 | 0 | 1 | 0 | 3 | 0 | 0 | 0 | 1 | 44 | 3 | 11 | 21 | 53 | 0 | 0 | 39 | 0 | 26 | 29 | 0 | 0 | 0 | 3 | 1 | 2 | 36 | 0 | 19 | 27 | 0 | 2 | 0 | 0 | 0 | 5 | 0 | 29 | 0 |
| 1 | 37098064 | 1 | 1 | 8 | 0 | 0.16181316 | 344 | 5 | 2 | 1 | 76 | 49 | 1 | 2 | 14 | 0 | 24 | 2 | 87 | 57 | 8 | 12 | 9 | 121 | 109 | 35 | 3 | 53 | 13 | 8 | 8 | 504 | 4 | 215 | 94 | 291 |
- Install Anacaonda for python 3: https://anaconda.org/anaconda/python
- (To check what version of python you have type
python --version)
- MUST CREATE A FILE CALLED config.ini FOR RUNTIME PARAMETERS
- set config.ini with these parameters:
[DEFAULT]
allelefreq cutoff = 0.5
min locus distance = 10
recombination_rate = 1e-8
minChrom = 1
filename = vcfDownloadTestData/CEU.exon.2010_03.genotypes.vcf
refPopulationNames = NA121,NA122,NA123
samplePopulationNames = NA124,NA125,NA127,NA128,NA10,NA11,NA120
refPopulationColumnIndices =
samplePopulationColumnIndices = - Then type in command line:
python createAncestryHMM-Input.py - Type a name for output at prompt
- Creates a tsv file with 136 lines
- To see it in terminal type:
cat <filename>
To use this program, edit config.ini for your input file in VCF format
[allelefreq cutoff]
- (Float) cutoff value for reference panel allele frequency calculation
[min locus distance]
- (Integer) minimum distance between each allele locus
[number of reference panels]
- (Integer) number of reference panel columns in the VCF.
[recombination_rate]
- (Float) estimated recombination rate for recombination probability for Ancestry_HMM input.
- Average recombinations per base pairs
[minChrom]
- (Integer) the minimum amount of chromosomes that must be present in the reference panel alleles to make it through the threshold
[filename]
- (String no quotes) Name of VCF file on local machine
There must be at least a reference and panel specified each in one of two ways
[refPopulationNames]
- (at least 2 Strings no quotes) Names of reference panels in the VCF file.
- Reference panels should be named like guanaco0 guanaco1 guanaco2 etc.
- Example argument: guanaco,vicugna
[samplePopulationNames]
- (at least 2 Strings no quotes) Names of sample panels to be run in Ancestry_HMM.
- Should be named like llama1 llama2 llama3 etc.
- Example argument: llama,alpaca
[refPopulationColumnIndices]
- Column index of reference panels to be run in Ancestry_HMM.
- [Syntax] beginning,end;beginning,end;...
- Example argument: 46,49;50,58;59,64
[samplePopulationColumnIndices]
- Column index of sample panels to be run in Ancestry_HMM.
- [Syntax] beginning,end;beginning,end;...
- Example argument: 69;70,82;83,98