Hi there,

I am trying to call SNPs, but only for 41 specific recognized ones (HIrisPlex-S). I have done this successfully with bcftools but now have to attempt it using freebayes. For bcftools, I was able to call all sites not just variants, and then use vcftools --positions and a text file with the SNP locations to filter it this way. Wondering if there is a similar way for me to do this with freebayes.

I currently have./freebayes -f ucsc.hg19.fasta sorted_WetSaliva_aligned_pairs.bam >freebayes_wetsaliva_calls.vcf but want to alter this so it is only the 41 SNPs.

Thanks