Using Snps And Indels To Create Reference Fasta

Question

[tinaw07]

Sorry if this is a repeat post but I can't seem to google an answer.

I was wondering what's everyone's favorite program is to generate a reference file from SNP and indel position data. I basically want to map these SNPs and indels of my mouse with the NCBI37 mm9 build and use this as a reference for downstream analysis.

Here is an excerpt of the kind of data I have. It's basically Chromosome/Position/ Reference at that site/ My individual at that site

1 3048072 T G

1 3062915 * +TT/+TT

1 3080344 C A

1 3084326 A G

1 3129698 T C

1 3157410 * -A/-A

Thank you for your time.

Answer 1

[Ashutosh Pandey]

Already answered

A: Substituting SNPs on reference genome assemblies

[tinaw07]

thanks for the help even though it's a repetitive question!

[Ashutosh Pandey]

No problem. You may have to convert your present format into psuedo vcf format.