samtools mpileup

[bair]

Hello all,

I'm using samtools-0.1.12a for snp calling from mutiple samples, after remove the INDELs ( varFilter applied), I find some snp have "N" as ref allele

1 145833120 . N T 11.10 . AF1=0.9402;CI95=0.0625,1;DP=4;DP4=0,0,0,2;GENE=NBPF1;MQ=49;TX=NBPF1:uc001emp.3:in12;TYPE=INTRONIC GT:GQ:PL 1/1:9:0,0,0 1/1:9:0,0,0 1/1:9:0,0,0 1/1:15:42,6,0 1/1:9:0,0,0 1/1:9:0,0,0 1/1:9:0,0,0 1/1:9:0,0,0

Why these loci with "N" as ref are treated as SNPs?

Many thanks

[nilshomer]

Looking in hg19, there is an N base in the reference.

[colindaven]

You can exclude these positions using the -N switch in bcftools view

-N skip sites where REF is not A/C/G/T