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 of Indel event based on the REF
How do I know based on the REF and ALT column of a VCF file the actual position where an indel event happened?
I usually see an event that occur in the 2nd base. For example,
GGCGTGGCGT G,GCGCGTGGCGT --deletion; insertion of "C"
ATTT A,ATT --deletions
But I saw a VCF format documentation(http://samtools.github.io/hts-specs/VCFv4.2.pdf) allowing a different case:
GTC G,GTCT --deletion; insertion of "T" at the end
How is UnifiedGenotyper formatting the indels? Does it differ
from the one used in the 1000Genome Project? Thank you!