Hello gatk community,
Since gatk haplotypecaller is ran by a sliding window approach, the variant calling on each position seems to also depend on the presence/type/absence of variants on the flanking region. I guess such effects will stem from the size used by the sliding window. For example, a longer flanking region that contains more variants will tend to help a new read to be better aligned on the current position as I suppose. Could you please let me know what is the internal sliding window size used by gatk HC?
Thank you!
Alice
