I'm dealing with GWAS data, I'm trying to Extract a list of all SNPs and their Values from the Bed file with Additive and dominance components using Python. Please help with the Python command to Extract all SNP id and their Values
>>> G = read_plink1_bin("Obesity_Send.bed", verbose=False)
Output:
xarray.DataArray'genotype'sample: 522variant: 2655566
Array Chunk
Bytes 5.16 GiB 2.04 MiB
Shape (522, 2655566) (522, 1024)
Count 10376 Tasks 2594 Chunks
Type float32 numpy.ndarray
Coordinates:
sample (sample) object '6' '74' '421' ... '433' '371' '47'
variant (variant) <U14 'variant0' ... 'variant2655565'
fid (sample) object '6' '74' '421' ... '433' '371' '47'
iid (sample) object '6' '74' '421' ... '433' '371' '47'
father (sample) object '0' '0' '0' '0' ... '0' '0' '0' '0'
mother (sample) object '0' '0' '0' '0' ... '0' '0' '0' '0'
gender (sample) object '2' '2' '2' '2' ... '1' '2' '2' '1'
trait (sample) object '2' '2' '2' '2' ... '-9' '-9' '-9'
chrom (variant) object '0' '0' '0' '0' ... '26' '26' '26'
snp (variant) object '200610-10' ... '200610-37'
cm (variant) float64 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0
pos (variant) int32 0 0 0 0 ... 16390 16391 16399 16482
a0 (variant) object '0' '0' '0' 'G' ... 'A' 'A' 'G' 'G'
a1 (variant) object 'A' 'A' 'A' 'A' ... 'G' 'G' 'A' 'A'
Desired Dataframe :
1. List of all SNPs with iid
2. Their allele values i.e a0 & a1