Question: GQ and DP filtering VCFtools
1
gravatar for swatipuraanik
3.1 years ago by
swatipuraanik30 wrote:

--minGQ <float> & --maxDP <float> options require that the GQ and DP FORMAT tag is specified for all sites. Can you please clarify that if ./. is present in any of columns in the format field, does it mean that GQ and DP are unspecified?

Sample 1                      Sample 2                                  Sample 3                      
GT:AD:DP:GQ:PL ./.                                      0/0:1,0:1:66:0,3,36                         ./.                       
GT:AD:DP:GQ:PL 0/0:2,0:2:79:0,6,72              0/0:1,0:1:66:0,3,36                        ./.                  
GT:AD:DP:GQ:PL ./.                                      ./.                                                 ./.                             
GT:AD:DP:GQ:PL 0/1:12,6:18:99:162,0,255     0/1:35,8:43:99:159,0,255              0/1:7,1:8:93:12,0,228 

Does it mean that commands like

vcftools --vcf all.taxamerged.vcf --minGQ x --recode --recode-INFO-all --out rawGQ

and

vcftools --vcf all.taxamerged.vcf --minDP y --recode --recode-INFO-all --out rawDP

will not work for filtering? Or am I giving any wrong commands?

Thanks

snp vcftools • 1.8k views
ADD COMMENTlink modified 3.1 years ago by RamRS22k • written 3.1 years ago by swatipuraanik30
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