Hey all,
When I use the following commands:
samtools mpileup -q 5 -Q 15 -l [interval_list] -AB -ugf [reference_sequence.fa] [aligned_file.bam] | bcftools view -bvcg -> [intermediate_file]
bcftools view -e [intermediate_file] | $vcfutils varFilter -D 99999 > [snps]
I will get output like this:
chr1 3354595 . T C 85 . DP=8;VDB=0.0404;AF1=0.5;AC1=1;DP4=1,2,0,5;MQ=60;FQ=47;PV4=0.38,1,1,1;AF1=0.5 GT:PL:GQ 0/1:115,0,74:77
Why does AF1 = 0.5 appear twice? Anybody have any idea?
- Ben
When I use the following commands:
samtools mpileup -q 5 -Q 15 -l [interval_list] -AB -ugf [reference_sequence.fa] [aligned_file.bam] | bcftools view -bvcg -> [intermediate_file]
bcftools view -e [intermediate_file] | $vcfutils varFilter -D 99999 > [snps]
I will get output like this:
chr1 3354595 . T C 85 . DP=8;VDB=0.0404;AF1=0.5;AC1=1;DP4=1,2,0,5;MQ=60;FQ=47;PV4=0.38,1,1,1;AF1=0.5 GT:PL:GQ 0/1:115,0,74:77
Why does AF1 = 0.5 appear twice? Anybody have any idea?
- Ben