I'm wondering what the best procedure for calling serial plasma samples from the same patients with a single normal sample would be.
For instance, running the samtools-mpileup-varscan2 pipeline with the normal sample first and the serial samples after gives genotype calls of 0/0 when I'd expect a variant to be called, such as here:
chr1 1471992 . T C . PASS ADP=14;WT=2;HET=2;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:23:23:23:16:7:30.43%:4.5803E-3:50:38:11:5:2:5 0/1:21:13:13:7:6:46.15%:7.4534E-3:34:35:2:5:1:5 0/0:3:10:10:6:4:40%:4.3344E-2:35:30:2:4:0:4 0/0:6:13:13:9:4:30.77%:4.7826E-2:30:30:5:4:1:3
in the fourth column (3rd serial plasma sample), when the read statistics are very similar to that in the second (1st serial sample) where the genotype has been called as 0/1.
Is this the best way of calling variants on multiple samples, or is it better to do normal/p1, normal/p2, normal/p3 etc, and then merge the variant sets at the end?