hi,all
Now,i have met a problem when using samtools to get SNP call. In the vcf file generated from samtools, i find high_quality bases so little in col(DP4=0,0,21,15), although coverage is very high(DP=5773). Then i check the sam file, and find that reads' BQ are almost high.
So,i want to know why .
The command:
mpileup -DugS -C 50 -f scaffold.fa all.bam |bcftools view -bcvg -> all.var.bcf
bcftools view all.var.bcf | vcfutils.pl varFilter > all.var.flt.vcf
The vcf file(partical):
gi|158420570|ref|NC_009938.1| 115 . C T,A 168 . DP=5773;VDB=0.0472;AF1=1;AC1=2;DP4=0,0,21,15;MQ=36;FQ=-132 GT:PLP:SP:GQ 1/1:201,105,0,183,71,180:36:0:99
gi|158420570|ref|NC_009938.1| 784 . G A 177 . DP=6382;VDB=0.0444;AF1=1;AC1=2;DP4=2,1,145,11;MQ=36;FQ=-282;PV4=0.21,9.3e-10,0.29,1 GT:PLP:SP:GQ 1/1:210,255,0:159:7:99
Now,i have met a problem when using samtools to get SNP call. In the vcf file generated from samtools, i find high_quality bases so little in col(DP4=0,0,21,15), although coverage is very high(DP=5773). Then i check the sam file, and find that reads' BQ are almost high.
So,i want to know why .
The command:
mpileup -DugS -C 50 -f scaffold.fa all.bam |bcftools view -bcvg -> all.var.bcf
bcftools view all.var.bcf | vcfutils.pl varFilter > all.var.flt.vcf
The vcf file(partical):
gi|158420570|ref|NC_009938.1| 115 . C T,A 168 . DP=5773;VDB=0.0472;AF1=1;AC1=2;DP4=0,0,21,15;MQ=36;FQ=-132 GT:PLP:SP:GQ 1/1:201,105,0,183,71,180:36:0:99
gi|158420570|ref|NC_009938.1| 784 . G A 177 . DP=6382;VDB=0.0444;AF1=1;AC1=2;DP4=2,1,145,11;MQ=36;FQ=-282;PV4=0.21,9.3e-10,0.29,1 GT:PLP:SP:GQ 1/1:210,255,0:159:7:99
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