Hi there!! I wanted to ask if there is a way to find shared SNPs between 4 different vcf files created from different library using the same de novo assembly. Supertranscript method was used in order to create a "reference" for the GATK pipeline. I filtered out only the heterozygous SNPs but now I want to compare which SNPs are shared among my 4 libraries/treatments. I tried to do
vcftools --vcf ./snps_filt_lib05.recode.vcf --diff ./snps_filt_lib02.vcf --diff-site --out snps_shared_lib02_vs_lib05
but i get the following error
Found TRINITY_DN9213_c0_g2 in file 1 and TRINITY_DN15627_c1_g1 in file 2. Use option --not-chr to filter out chromosomes only found in one file.
The --not-chr filter, if I got it correctly, requires to know a priori which chromosoms (trinity genes) you want to exclude. Moreover, I cannot find any vcf-compare comands in v. 0.1.15 that I use. Any help would be apreciated Thanks a lot!1