How can I merge multiple GBS data sample into one?

Question

[anjun.ma]

Hi all,

I have several maize GBS raw data (less than 10) from the same family. I wish to merge these individual sequence into one ., meanwhile fix and patch the mistakes of SNPs.

For example:

sample 1: NNNNN TTCGG TNNGC sample 2: NNNNN TTCCC TNNGC sample 3: NNANN NTCGG TNNGC

merge and fix to: NNNNN TTCGG TCCGC

Once the SNP shows up in 2 samples then considered as a real SNP otherwise no change.

I'm new in GBS and SNP analysis. Can someone help me with this? Thank you!

PS: I've already separate each sample sequence into individual fasta file and barcode is removed.I know statistically using such a small population to do this is meaningless, let's just say this is a test. :)

Anjun