Hi all,
I'm using samtools to find variants in my resequencing data, and I've noticed something weird:
After running the following command:
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.
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):
Anybody knows what's going on? I've never seen this behavior before with Samtools.
Thanks,
Rachelly.
I'm using samtools to find variants in my resequencing data, and I've noticed something weird:
After running the following command:
Code:
samtools mpileup -L 10000 -d 10000 -ugEf <my_genome> <my sorted BAM> | bcftools view -g - > samp.raw.vcf
Code:
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
Code:
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
Thanks,
Rachelly.
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