I have a dbSNP annotated SNP calls file. The file contains following columns:
Hugo_Symbol Entrez_Gene_Id Chromosome Start_position End_position Strand Variant_Classification Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS Genome_Change Annotation_Transcript Transcript_Strand cDNA_Change Codon_Change Protein_Change NP_id NP_region(note) NP_bond NP_site CDD_structure_id cosmic_total_mutations_in_gene
Now I want to get the genotype for the individual snps in this data.
How can I do this??
I think you're not getting any answers because the question is very unclear.
Unless I'm missing something, the only way to determine the genotype is to look at what is reported in the "Tumor_Seq_Allele1" and "Tumor_Seq_Allele2" columns of your MAF file.
Having said this, I'm confused as to why you have not considered looking at the allele columns and I'm even more confused as to how you could use dbSNP in any way to determine the genotype of your snps, so I may be misunderstanding what you are looking for.
@Pierre I tried dbsnp but it is tedious for large data.
@nielfws
MYPN 84665 broad.mit.edu 37 chr10 69933969 69933969 + Missense_Mutation SNP G A A rs7916821 by-cluster,by-frequency,by-2hit-2allele,by-hapmap,by-1000genomes normal normal Unknown Unknown Unknown Phase_I Capture Illumina_GAIIx g.chr10:69933969G>A NM_032578.2 + c.2120G>A c.(2119-2121)AGT>AAT p.S707N NP_115967.2 None None None None 0 --- --- 0
TACC2 10579 broad.mit.edu 37 chr10 123846490 123846490 + Missense_Mutation SNP C T T rs7920896 by-cluster,by-frequency,by-hapmap,by-1000genomes normal normal Unknown Unknown Unknown Phase_I Capture Illumina_GAIIx g.chr10:123846490C>T NM_206862.2 + c.4475C>T c.(4474-4476)CCA>CTA p.P1492L NP_996744.2 None None None None 0 --- --- 4
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what did you try so far ?
It helps to see some of the data in addition to the header line.
@Pierre I tried dbsnp but it is tedious for large data.
MYPN 84665 broad.mit.edu 37 chr10 69933969 69933969 + Missense_Mutation SNP G A A rs7916821 by-cluster,by-frequency,by-2hit-2allele,by-hapmap,by-1000genomes normal normal Unknown Unknown Unknown Phase_I Capture Illumina_GAIIx g.chr10:69933969G>A NM_032578.2 + c.2120G>A c.(2119-2121)AGT>AAT p.S707N NP_115967.2 None None None None 0 --- --- 0