Dear people I have used lofreq for variant calling. My VCF files do no have sample name column.
> #CHROM POS ID REF ALT QUAL FILTER INFO chr1 1120488 . A C 2383 PASS DP=150;AF=0.513333;SB=0;DP4=29,44,30,47;ANNOVAR_DATE=2018-04-16;ExAC_ALL=0.0064;ExAC_AFR=0.0658;ExAC_AMR=0.0029;ExAC_EAS=0;ExAC_FIN=0;ExAC_NFE=0.0008;ExAC_OTH=0.0035;ExAC_SAS=6.118e-05;Func.refGene=exonic;Gene.refGene=TTLL10;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=TTLL10:NM_153254:exon9:c.A1181C:p.K394T,TTLL10:NM_001130045:exon13:c.A1400C:p.K467T;ALLELE_END >
I will have to input them into PLINK but unfortunatly I cant even using allow-no-samples.
I would really appreaciate if some one could help me turning my VCFs into normal! by adding sample name column.
I also can not using the merge function of BCFtools or VCFtools.
Best regards Mo