vcftools DP filter error

Question

[sun.nation]

I used this command:

vcftools --vcf cotton2.all.bcf.vcf --out cotton2.all.bcf.vcf.maf1.vcf \
--remove-filtered-all --max-missing-count 0 --minDP 10 --minQ 10 \
--maxDP 1000 --maf 1.0 --recode --recode-INFO-all

to filter SNPs with less than 10 reads but still got SNPs with < 10 DP.

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  cotton2.jgi.bam.sorted.bam`
scaffold_100    2922    .       A       G       152     .       DP=7;VDB=4.917119e-03;AF1=1;AC1=2;DP4=0,0,2,5;MQ=60;FQ=-48      GT:PL:DP:SP:GQ  ./.:185,21,0:7:0:39
scaffold_100    2939    .       A       G       16.1    .       DP=7;VDB=7.200000e-02;RPB=9.837446e-01;AF1=0.5;AC1=1;DP4=2,3,0,2;MQ=60;FQ=19.1;PV4=1,1,1,0.24  GT:PL:DP:SP:GQ  ./.:46,0,137:7:0:49
scaffold_100    2946    .       C       T       152     .       DP=7;VDB=7.443299e-02;AF1=1;AC1=2;DP4=0,0,2,5;MQ=60;FQ=-48      GT:PL:DP:SP:GQ  ./.:185,21,0:7:0:39
scaffold_100    3038    .       T       A       48      .       DP=3;VDB=2.309944e-02;AF1=1;AC1=2;DP4=0,0,1,2;MQ=60;FQ=-36      GT:PL:DP:SP:GQ  ./.:80,

Is there any error that I am making? Thanks

Answer 1

[Brice Sarver]

I believe the DP here is a genotype-level filter, so you want --remove-filtered-geno-all instead of --remove-filtered-all, which is a site-level filter.

[sun.nation]

Using --remove-filtered-geno-all didn't help either. It gave the same output.