Mpileup Vcf Multiple Variants At One Position
my workflow:
samtools mpileup -uDf ref.fa bamfile.bam | bcftools view -bvc > bcffile.bcf
bcftools view bcffile.bcf
gene1 32 . G T,C 999 . DP=5558;AF1=1;CI95=1,1;DP4=0,1,3543,0;MQ=44;FQ=-79;PV4=0.00028,1,1,3.5e-11 PL:DP 195,45,0,195,34,192:16 255,255,0,255,255,255:1656 255,255,0,255,255,255:1872
how can I tell how many times the variant is T and how many times the variant is C?
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Jeremy Leipzig
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ok I would guess from the last columns
16 high quality reference calls
1656 high quality T calls
1872 high quality C calls
that equals 3544
DP4 says there are:
1 high quality reverse reference call
3543 high quality forward non-reference calls
so I am not sure what 16, 1656, and 1872 represent
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Jeremy Leipzig
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