I have 10 different vcf files which are of different samples.
I want to find the SNPs common between all of them i.e the snp should be present in all the 10 samples.
For that I am using vcftools isec but I am getting 10 different files instead of one single file with the common snps.
The readme file says: 0000.vcf has stripped reads for sample 1 , 0001.vcf has stripped reads for sample 2 and so on.
The command used is:
/data/ngs/programs/bcftools-1.3/bcftools isec -p match/ -n=10 qual-out-1.vcf.recode.vcf.gz qual-out-2.vcf.recode.vcf.gz ... qual-out-10.recode.vcf.gz
I have obtained these files from GATK pipeline.My ultimate aim is to just get one single vcf with all common snps