VCF file
Removal Sample
###junk removal
vcftools --gzvcf cohorts_combined_filtered_calls_annotated.vcf --maf 0.05 --max-missing 0.8 --min-meanDP 10 --recode --out SNP-co.vcf
####Sample removal
bcftools view --samples-file ^ /media/bioinformatician/My\ Passport/sample_id_no-RNASEq.txt SNP-co.vcf.
###chromosome extraction
vcftools --gzvcf SNP_co.vcf.gz --chr 2 --from-bp 47843908 --to-bp 47877312 --recode --out snps_filt_chr2
##conversion vcf to plink
./plink --vcf /media/bioinformatician/My\ Passport/annotated/tabix/snps_filt_chr2.vcf.gz.recode.vcf --recode HV --out /media/bioinformatician/My\ Passport/annotated/tabix/chr2
PLINK v1.90p 64-bit (6 Jun 2021)
Logging to /media/bioinformatician/My Passport/annotated/tabix/chr2.log.
Options in effect:
--out /media/bioinformatician/My Passport/annotated/tabix/chr2
--recode HV
--vcf /media/bioinformatician/My Passport/annotated/tabix/snps_filt_chr2.vcf.gz.recode.vcf
31909 MB RAM detected; reserving 15954 MB for main workspace.
Error: No variants in VCF file.
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Ohh Sorry. The query was deleted out of that. I have vcf file, I want to remove some samples, filter junk and extract chr2 with specific position as vcf file to visualize in haploview. I executed above commands. I am getting error. Please help me.
IMO it seems your VCF files does not contain any variants at Chr2 47843908 - 47877312. Maybe try to use grep/awk to check manually if there is any position in this region showing a variant.
The variant is already known in this region. Previously it was giving an error there is no genotype.