I got a indel as following :
chr1 7096787 . C CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 48.5 . INDEL;DP=35;AF1=0.501;CI95=0.5,0.5;DP4=1,0,2,6;MQ=57;FQ=-10.9;PV4=0.33,0.14,0.37,0.13 GT:PL:GQ 0/1:86,0,24:27
above file is vcf formart. Does anybody know 'N' in fifth column?
variant calling commnads are the follwing :
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
chr1 7096787 . C CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 48.5 . INDEL;DP=35;AF1=0.501;CI95=0.5,0.5;DP4=1,0,2,6;MQ=57;FQ=-10.9;PV4=0.33,0.14,0.37,0.13 GT:PL:GQ 0/1:86,0,24:27
above file is vcf formart. Does anybody know 'N' in fifth column?
variant calling commnads are the follwing :
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
Comment