Question: Mpileup Vcf Multiple Variants At One Position
3
gravatar for Jeremy Leipzig
8.6 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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?

vcf samtools mpileup • 2.4k views
ADD COMMENTlink modified 8.3 years ago • written 8.6 years ago by Jeremy Leipzig18k
0
gravatar for Jeremy Leipzig
8.6 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by Jeremy Leipzig18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 730 users visited in the last hour