Hi, I would like to know if it is possible to get the strand information of the SNVs identified by mutect.
We follow the 1000 Genomes Project convention of reporting all variants on the forward strand.
Can you please clarify what you mean by "strand information"?
For example I have chr1 position 1000 in the mutect output but i do not find if it is in the minus or plus strand.
Thank you, if I used the dbSNP as database, in which there are SNPs annotated in plus and minus strand, I could consider all the positions in the mutect1 output annotated in the plus strand?