When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example:
Here is a real example for one indel (from the same sample) called by:
Samtools --> 1 161047125 CTATA C
GATK --> 1 161047130 TATAG T
I am wondering if someone knows what is the indel alignment direction in samtools, GATK and Dindel? Is there an easy way to correct this at level of VCF files?