Chasm

[kasthuri]

I have a bunch of mutations with Ensembl annotations for gene name and I am trying to run CHASM:

http://wiki.chasmsoftware.org/index.php/CHASM_Tutorial#Configuration_Options

It requires mutations defined as amino-acid residue substitutions, along with an accession identifier from NCBI RefSeq, CCDS, or Ensembl in the following format.

NP_001135977 R641W
NP_835455 R151C
NP_055645 L590V
NP_689808 D28H
NP_005472 S372R

Can somebody help me how to get this annotation (as amino-acid residue substitutions and accession identifier) for my Ensembl mutation list?

Thanks
-Kasthuri

[bio_informatics]

You can use online version of Chasm. If you have annotated vcf file.

If the file is of few mega bytes ~80-100 mbs, you would have your output in less than 30 mins.