I have analyzed SNP in two contrasting genotypes based on RNAseq data using GATK pipeline. In some cases, there is a string of nucleotide in the reference position and the only single alternate nucleotide in genotype. what does it mean?
After calling SNP by using GATK, How should I filter raw VCF to find only confirmed SNP?
CHROM POS ID REF ALT QUAL FILTER INFO R1 1119 . C T 311.78 . R1 1132 CACTTGG C 302.75 . R1 1275 .T C 146.9 . .