trying to split vcf file into samples and control

[SamahElmahdi]

i have tried to split the compined vcf into samples and control to compare the count of known and novel varients in each of them.

bcftools view -s SRR5858157_F8_III.4,SRR5858162_F8_III.3,SRR5858204_F6_II.2 raw_variants_ann.vcf > raw_variants_ann_samples.vcf
bcftools view -s SRR5858160_F7_II.3,SRR5858161_F7_II.2 raw_variants_ann.vcf > raw_variants_ann_controls.vcf
grep -v "^#" raw_variants_ann_controls.vcf | awk '{print $3}' | wc -l ###total35472
grep -v "^#" raw_variants_ann_controls.vcf | awk '{print $3}' | grep "^rs" | wc -l ###known10900
grep -v "^#" raw_variants_ann_samples.vcf | awk '{print $3}' | wc -l ###total35472
grep -v "^#" raw_variants_ann_samples.vcf | awk '{print $3}' | grep "^rs" | wc -l ###Known10900
the nos are equal and i think that there is something wrong in my code but i really don't have time to try to solve it as today is the dead line and we can calculate them from the state file created before.
these links was helpful

1. https://bioinformatics.stackexchange.com/questions/3477/how-to-subset-samples-from-a-vcf-file
2. https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=f667c2ee6f2ca971&tool_config=%2Fsrv%2Ftoolshed%2Fmain%2Fvar%2Fdata%2Frepos%2F002%2Frepo_2516%2Fbcftools_view.xml&changeset_revision=cc016cb332cd

[SamahElmahdi]

another method :
cat raw_variants_ann.vcf |cut -f3| grep "^rs" > raw_variants_ann_knownIDs.txt
vcftools --vcf raw_variants_ann_samples.vcf --snps raw_variants_ann_knownIDs.txt --recode --recode-INFO-all --stdout > raw_variants_ann_samples_known.vcf
vcftools --vcf raw_variants_ann_controls.vcf --snps raw_variants_ann_knownIDs.txt --recode --recode-INFO-all --stdout > raw_variants_ann_controls_known.vcf
wc -l raw_variants_ann_samples_known.vcf ####10944
wc -l raw_variants_ann_controls_known.vcf ####10944
same no of each one!!
may be the problem is in the splitting file step !!!