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Old 04-03-2012, 05:23 AM   #1
Location: Israel

Join Date: Oct 2010
Posts: 37
Default VCF file - no ALT but DP4 alternative exist

Hi all,

I'm using samtools to find variants in my resequencing data, and I've noticed something weird:

After running the following command:
samtools mpileup -L 10000 -d 10000 -ugEf <my_genome> <my sorted BAM> | bcftools view -g - > samp.raw.vcf
I got a line in the VCF file that doesn't make sense: It said that there is no variant (ALT=".", AF1="0"), but there are alternative alleles, as can be seen in the DP4 attributes. I also see it clearly in the IGV when viewing the BAM file.

genome     197469  .       T       .       72      .       DP=666;VDB=0.0469;AF1=0;AC1=0;DP4=258,220,75,110;MQ=33;FQ=-69;PV4=0.0024,1,3.4e-120,1   PL      0
And the weirdest thing is that when I ran the same command on a different sample, the output was ok (both samples contain the same SNP):
genome     197469  .       T       C       27      .       DP=666;VDB=0.0469;AF1=0.5;AC1=1;DP4=258,220,75,110;MQ=33;FQ=30;PV4=0.0024,1,3.4e-120,1  GT:PL:GQ        0/1:57,0,255:60
Anybody knows what's going on? I've never seen this behavior before with Samtools.

Rachelly is offline   Reply With Quote
Old 04-03-2012, 09:17 AM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

What does the pileup look like at that locus?
swbarnes2 is offline   Reply With Quote
Old 04-04-2012, 03:12 AM   #3
Location: Israel

Join Date: Oct 2010
Posts: 37
Default The pileups looks the same..

The pileup of both samples looks exactly the same. See the attached image from IGV.


I found more examples for this behavior in these samples, where they look the same in IGV but their VCF files look different:

genome     256638  .       C       .       82      .       DP=702;VDB=0.0188;AF1=0;AC1=0;DP4=319,217,94,70;MQ=33;FQ=-79;PV4=0.65,1,1.3e-98,1       PL      0
genome     256638  .       C       A       4.77    .       DP=702;VDB=0.0188;AF1=0.4999;AC1=1;DP4=319,217,94,70;MQ=33;FQ=6.99;PV4=0.65,1,1.3e-98,1 GT:PL:GQ        0/1:33,0,255:33
genome     217418  .       A       .       15.1    .       DP=940;VDB=0.0028;AF1=0.492;AC1=1;DP4=316,372,116,121;MQ=33;FQ=-12.3;PV4=0.45,2.7e-05,9.7e-135,4.6e-10  PL      15
genome     217418  .       A       T       5.46    .       DP=940;VDB=0.0028;AF1=0.4999;AC1=1;DP4=316,372,116,121;MQ=33;FQ=7.8;PV4=0.45,2.7e-05,9.7e-135,4.6e-10   GT:PL:GQ        0/1:34,0,255:34
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