Friday, January 8, 2016

COSMIC genotype


gunzip 1240121_complexGenotypes.csv.gz

Byte-4:genotypes hqin$ wc -l 1240121_complexGenotypes.csv

  884149 1240121_complexGenotypes.csv
There are 884K rows of SNPs in this file. 


Files listing the SNP calls for each cell line identified by PICNIC analysis of
Affymetrix SNP6.0 array data. Both a simple genotype (AA, BB – homozygous or AB
– heterozygous) and a complex interpretation of the genotype are given (for
example, in a triploid region of the genome the genotype maybe AAB). 

Download from genotypes directory.

File Description

Chr - Chromosome GRCh38/hg38

pos - Genome Position GRCh38/hg38
ncopies.A - Number of copies of allele A
ncopies.B - Number of copies of allele B
Probe.Set.ID - SNP6.0 probe ID
dbSNP.RS.ID - dbSNP reference ID
Allele.A - genotype 'A' nucleotide
Allele.B - genotype 'B' nucleotide
chr_b36 - Chromosome NCBI36/hg18
pos_b36 - Genome Position NCBI36/hg18
chr_b37 - Chromosome GRCh37/hg19
pos_b37 - Genome Position GRCh37/hg19
complexGenotype - a complex interpretation of the genotype eg in a triploid
region the genotype maybe AAB
simpleGenotype - a simple genotype eg AA, BB – homozygous or AB –

No comments:

Post a Comment