How To Get Snp Genotypes

Question

[Pri]

I have a annotated snp annotated file. This file contains dbsnp id, chromosome, position reference allele and tumor allele columns. How can i get genotype in the form ie AA, BB, AB etc on these files.

SAMPLE FILE:

Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Sequence_Source Sequencer 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_mutations_within_0_bp cosmic_samesub|diffsub|indel_or_diffAA|unknown cosmic_total_mutations_in_gene 

TP53 7157 37 chr17 7578525 7578525 + Nonsense_Mutation SNP G T T novel none normal normal Capture Illumina_GAIIx g.chr17:7578525G>T NM_001126112.1 - c.405C>A c.(403-405)TGC>TGA p.C135* NP_001119584.1 P53(P53_DNA-binding_domain;_cd08367) None None CDD:176262 TP53(4) 0|0|1|3 21274

PTPN11 5781 37 chr12 112892407 112892407 + Missense_Mutation SNP T G G novel none normal normal Capture Illumina_GAIIx g.chr12:112892407T>G NM_002834.3 + c.565T>G c.(565-567)TCT>GCT p.S189A NP_002825.3 SH2(Src_homology_2_domains;_Signal_transd...) None hydrophobic_binding_pocket CDD:29135 0 --- 378

[Thaman]

Then you should!

[Pierre Lindenbaum]

@pri http://korflab.ucdavis.edu/Unix_and_Perl/

[Neilfws]

You need to show us some sample lines from the file before we can help.

[Jorge Amigo]

thanks for such great resource Pierre. I've forwarded it to my biology colleagues ;)

[Jorge Amigo]

please read again neilfws' first comment, requesting some sample lines in order to understand the data format you're dealing with. you may edit your own question by attaching such lines.

[Jorge Amigo]

we need to see an example of your data to check if the genotypes are present on that annotation file of yours, because if not you'll have to return to the original source of your data and look for genotypes there.

[Pri]

i have the genotypes in my file ie the tumor_allele column. my question is how do i get this in AA AB BB format. What is the way to do this??

[Pierre Lindenbaum]

what did you try so far ?

[Pri]

i've not tried anything yet

[Pri]

what should i try?

[Chris Evelo]

Pierre that is not a comment but an answer :)