no samples in vcf file

[test1]

I am trying to convert vcf file generated for HRC dataset to binary plink file format but it gives error "no samples in .vcf file"

please helps

thank you

[Christopher Chang]

What does the top of the VCF file look like (up to one line after the #CHROM  POS  ID  ... line)?

[test1]

this is the top section:

##fileformat=VCFv4.1       
##FILTER=<ID=PASS,Description="All filters passed">       
##contig=<ID=1,length=249250621>       
##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate allele count in called genotypes">       
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">       
##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency from called genotypes">       
##INFO=<ID=AC_EXCLUDING_1000G,Number=A,Type=Integer,Description="Alternate allele count in called genotypes excluding 1000G samples">       
##INFO=<ID=AN_EXCLUDING_1000G,Number=1,Type=Integer,Description="Total number of alleles in called genotypes excluding 1000G samples">       
##INFO=<ID=AF_EXCLUDING_1000G,Number=A,Type=Float,Description="Alternate allele frequency from called genotypes excluding 1000G samples">       
##contig=<ID=2,length=243199373>       
##contig=<ID=3,length=198022430>       
##contig=<ID=4,length=191154276>       
##contig=<ID=5,length=180915260>       
##contig=<ID=6,length=171115067>       
##contig=<ID=7,length=159138663>       
##contig=<ID=8,length=146364022>       
##contig=<ID=9,length=141213431>       
##contig=<ID=10,length=135534747>       
##contig=<ID=11,length=135006516>       
##contig=<ID=12,length=133851895>       
##contig=<ID=13,length=115169878>       
##contig=<ID=14,length=107349540>       
##contig=<ID=15,length=102531392>       
##contig=<ID=16,length=90354753>       
##contig=<ID=17,length=81195210>       
##contig=<ID=18,length=78077248>       
##contig=<ID=19,length=59128983>       
##contig=<ID=20,length=63025520>       
##contig=<ID=21,length=48129895>       
##contig=<ID=22,length=51304566>       
##contig=<ID=X,length=155270560>       
##contig=<ID=Y,length=59373566>       
##contig=<ID=MT,length=16569>       
##bcftools_viewVersion=1.3+htslib-1.3       
##bcftools_viewCommand=view -Ou -S ^hrc.gecco.remove.samples --force-samples /lustre/scratch114/projects/hrc/hrc-dropbox/panels/HRC.r1.20150417/vcf/HRC.r1.GRCh37.chr1.shapeit3.mac5.genotypes.bcf       
##bcftools_pluginVersion=1.3-31-g014c136-dirty+htslib-1.3-37-gfc93dfc       
##bcftools_pluginCommand=plugin aggregate -Ou -- -Ut AC,AN,AF -S excluding_1000g.samples       
##bcftools_viewCommand=view -Ou -c5:minor       
##bcftools_annotateVersion=1.3+htslib-1.3       
##bcftools_annotateCommand=annotate -Ou -a /lustre/scratch116/vr/ref/human/GRCh37/resources/dbsnp/dbsnp_142.b37.tab.gz -c CHROM,POS,ID,REF,ALT       
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral allele">       
##bcftools_pluginCommand=plugin fill-from-fasta --threads 16 -Ob -o /lustre/scratch116/vr/projects/hrc/hrc-dropbox/panels/HRC.r1.20160326/vcf/HRC.r1-1.GRCh37.chr1.shapeit3.mac5.aa.genotypes.bcf -- -c AA -h /lustre/scratch116/vr/ref/human/GRCh37/resources/anno/human_ancestor.fa.gz.hdr -f /lustre/scratch116/vr/ref/human/GRCh37/resources/anno/human_ancestor.fa.gz       
##bcftools_viewCommand=view -GOb HRC.r1-1.GRCh37.chr1.shapeit3.mac5.aa.genotypes.bcf       
##bcftools_convertVersion=1.2+htslib-1.2.1       
##bcftools_convertCommand=convert --hapsample2vcf - -Ob -o /net/fantasia/home/sayantan/GLOBUS_DOWNLOAD/tarballs/hrc.r1.genotype_calling-20151110/results/BCF_FIN/HRC.r1.chr9.before.jitter.bcf.gz       
##vcfJitterPos_version=0.001       
##vcfJitterPos_command=-r /net/fantasia/home/sayantan/GLOBUS_DOWNLOAD/tarballs/hrc.r1.genotype_calling-20151110/work/offset/gls/9.gls.jitter.bcf.map       
##bcftools_concatVersion=1.3+htslib-1.3       
##bcftools_concatCommand=concat -Oz -f concat.list       
#CHROM POS ID REF ALT QUAL FILTER INFO
1 13380 rs571093408 C G . . AC=5;AN=64940;AF=7.69941e-05;AC_EXCLUDING_1000G=0;AN_EXCLUDING_1000G=59950;AF_EXCLUDING_1000G=0;AA=.

[Christopher Chang]

Well, there actually aren't any samples in this file...

[test1]

so when I only need bim (marker files) from a vcf , I can not use plink-vcf option?...ok, thanks

[Christopher Chang]

You can use --allow-no-samples during VCF import if that's really what you want.

[test1]

thank you...yes, that's what I need!

best

On Thursday, April 20, 2017 at 4:52:03 PM UTC-4, test1 wrote: