Hey guys,
I am new to vcf and having difficulty filtering my SNPs in vcfTools.
I have a vcf file (fileformat=VCFv4.1) of SNPs found in a group of individuals of a species (pooled as one individual for the time being).
sample:
Spp1_cDNA-30 211 . G A 122 . DP=15;VDB=0.0017;AF1=1;AC1=2;DP4=0,0,0,12;MQ=60;FQ=-63 PL 155,36,0
I want to apply some simple filters e.g. depth.
However the output file generated gives me depths of 0 at all SNPs despite the vcf giving sensible DP values.
Similarly, mean depth stat calculation returns 0 for the entire vcf.
What am I doing wrong here guys?
Any help will be much appreciated.
Thanks,
J
I am new to vcf and having difficulty filtering my SNPs in vcfTools.
I have a vcf file (fileformat=VCFv4.1) of SNPs found in a group of individuals of a species (pooled as one individual for the time being).
sample:
Spp1_cDNA-30 211 . G A 122 . DP=15;VDB=0.0017;AF1=1;AC1=2;DP4=0,0,0,12;MQ=60;FQ=-63 PL 155,36,0
I want to apply some simple filters e.g. depth.
However the output file generated gives me depths of 0 at all SNPs despite the vcf giving sensible DP values.
Similarly, mean depth stat calculation returns 0 for the entire vcf.
What am I doing wrong here guys?
Any help will be much appreciated.
Thanks,
J
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