Hello,

I am implementing my pipeline for Roche 454 Junior 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 position 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 you please help me?