Entering edit mode
7.8 years ago
swatipuraanik
▴
30
--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