How to identify each sample?

[FerVallejoLec]

Hi
I was wondering if I could kwon which variations are in each sample.

Thanks.

[tdelhomme]

Hi,

Actually needlestack returns a multi sample VCF file, so each line corresponds to a particular mutation and each column to a sample, i.e. to the status of the sample for the mutation (see the format field).

You can filter out the VCF for a particular sample using bcftools -s, and after that you can use bcftools filter (manual) to filter on the QVAL field to keep only mutated positions on this sample. The QVAL field corresponds to the "probability" of being mutated.

Do not hesitate to ask if something is still unclear!