position indel, variant calling
I am implementing my pipeline for Roche 454 and I have used GATK for called of variants.
I have compared my variants with Roche's variants and for BRCA1 my variants corresponded, but the position of indel for BRCA2 are wrong, the vcf file reported that them position is a few bp before (instead the positions of snp are right)
I have searched on genome browser and I have seen that the positions of Roche were right.
For example, this are the coordinates that I have in my files.
Roche GATK VARIANT
32893207 32893197 T/-
32900342 32900337 A/-
32900370 32900363 T/-
32900376 32900371 C/-
32900933 32900933 T/A
32907208 32907202 A/-
32907428 32907420 A/-
32907546 32907535 TTT/-
Could help me?