Hi, I have used the samtools for SNP calling for my wheat GBS data, after filtration what I got is 'N' against any ref allele in P1 and the same ref allele in P2 and so is the case with progeny. I am new to this bioinfo analysis. If you know the loophole please suggest me.
Thanks in advance *Ankita Mishra* *DST- Inspire Fellow* *National Agri-food Biotechnology Institute* *Mohali- 140306* *Punjab* [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&;> 02/20/19, 7:20:49 PM
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