COSMIC genotype

v75
~/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. 

Genotypes

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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 –

heterozygous