VQSR for multiple small target sequencing samples
We are developing analysis pipeline for our small target sequencing samples (target coding exons of 30 genes). We have 84 samples, sequenced from one lane of GAII. There are around 100 ~ 200 variants in one sample. From the best practice, the way to do it is to call variants on 84 samples together, then use VQSR on one single vcf to do soft filtering. I feel the number of variants (maybe still hundreds of variants) will be not enough for training the model. Instead of calling variants on 84 samples together, I called variants on each sample and then do VQSR on 84 vcf files, the VQSR was passed through and get better results compared with hard filtering. I just wonder whether my way is reasonable?
Thanks in advance for the comments