The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?