Hey,
I'm running mpileup to generate a consensus sequence and when I run it and convert it to .vcf format, I see many indels that match the following sequence. My command line and an example of the odd indel is below:
samtools mpileup -Q 25 -d 40000 -uf ref.fa in.bam | bcftools view -cg - > out.vcf
gi|223976078|ref|NC_012095.1| 5988 . CTTTTTT . 99 . INDEL;DP=39134;AF1=0;CI95=1.5,0;DP4=14546,15887,67,67;MQ=60;PV4=0.66,1,1,0.028 PL 0
gi|223976078|ref|NC_012095.1| 5989 . T . 99 . DP=39199;AF1=0;CI95=1.5,0;DP4=18087,20153,0,0;MQ=60 PL 0
gi|223976078|ref|NC_012095.1| 5990 . T . 99 . DP=39116;AF1=0;CI95=1.5,0;DP4=17719,20059,0,0;MQ=60 PL 0
gi|223976078|ref|NC_012095.1| 5991 . T . 99 . DP=39395;AF1=0;CI95=1.5,0;DP4=16529,18557,1,0;MQ=60;PV4=0.47,2.4e-05,1,0.073 PL 0
gi|223976078|ref|NC_012095.1| 5992 . T . 99 . DP=39105;AF1=0;CI95=1.5,0;DP4=16713,18665,0,0;MQ=60 PL 0
gi|223976078|ref|NC_012095.1| 5993 . T . 99 . DP=38041;AF1=0;CI95=1.5,0;DP4=17015,19513,0,1;MQ=60;PV4=1,0.00047,1,1 PL 0
gi|223976078|ref|NC_012095.1| 5994 . T . 99 . DP=38046;AF1=0;CI95=1.5,0;DP4=17325,19918,2,0;MQ=60;PV4=0.22,5.4e-07,1,0.19 PL 0
As you can see, the "deletion" sequence "CCCCCC" matches the following sequence, making me think it's not real. I see this same pattern numerous times.
Any ideas what is going on here?
Thanks,
Matt
I'm running mpileup to generate a consensus sequence and when I run it and convert it to .vcf format, I see many indels that match the following sequence. My command line and an example of the odd indel is below:
samtools mpileup -Q 25 -d 40000 -uf ref.fa in.bam | bcftools view -cg - > out.vcf
gi|223976078|ref|NC_012095.1| 5988 . CTTTTTT . 99 . INDEL;DP=39134;AF1=0;CI95=1.5,0;DP4=14546,15887,67,67;MQ=60;PV4=0.66,1,1,0.028 PL 0
gi|223976078|ref|NC_012095.1| 5989 . T . 99 . DP=39199;AF1=0;CI95=1.5,0;DP4=18087,20153,0,0;MQ=60 PL 0
gi|223976078|ref|NC_012095.1| 5990 . T . 99 . DP=39116;AF1=0;CI95=1.5,0;DP4=17719,20059,0,0;MQ=60 PL 0
gi|223976078|ref|NC_012095.1| 5991 . T . 99 . DP=39395;AF1=0;CI95=1.5,0;DP4=16529,18557,1,0;MQ=60;PV4=0.47,2.4e-05,1,0.073 PL 0
gi|223976078|ref|NC_012095.1| 5992 . T . 99 . DP=39105;AF1=0;CI95=1.5,0;DP4=16713,18665,0,0;MQ=60 PL 0
gi|223976078|ref|NC_012095.1| 5993 . T . 99 . DP=38041;AF1=0;CI95=1.5,0;DP4=17015,19513,0,1;MQ=60;PV4=1,0.00047,1,1 PL 0
gi|223976078|ref|NC_012095.1| 5994 . T . 99 . DP=38046;AF1=0;CI95=1.5,0;DP4=17325,19918,2,0;MQ=60;PV4=0.22,5.4e-07,1,0.19 PL 0
As you can see, the "deletion" sequence "CCCCCC" matches the following sequence, making me think it's not real. I see this same pattern numerous times.
Any ideas what is going on here?
Thanks,
Matt
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