Genotypes For Snps

Question

[Rima]

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??

[Pierre Lindenbaum]

what did you try so far ?

[Neilfws]

It helps to see some of the data in addition to the header line.

[Rima]

@Pierre I tried dbsnp but it is tedious for large data.

[Rima]

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

Answer 1

[Nina]

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.

Answer 2

[Rima]

@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

[Pierre Lindenbaum]

This is not an answer. Please, delete this post and update your original question.