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Old 03-02-2011, 04:39 AM   #1
bair
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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
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Old 03-02-2011, 11:37 PM   #2
nilshomer
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Looking in hg19, there is an N base in the reference.
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Old 03-03-2011, 03:38 AM   #3
colindaven
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You can exclude these positions using the -N switch in bcftools view

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