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