Mpileup Vcf Multiple Variants At One Position

Question

[Jeremy Leipzig]

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?

Answer 1

[Jeremy Leipzig]

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