Help with interval list

[vappiah]

Dear Team.
I recently used gatk to run haplotype caller. I used an interval file in the bed format. Instead of offsetting the position by 1 I used the actual positions. Does it mean that gatk processed the information by adding +1 to the generated VCF file.?

If so how can I offset the position by 1 in the generated vcf.

PS.
It took several days to run haplotype caller and I will be happy if I can deal with this without rerunning due to time constraint.
Thanks

[gokalpcelik]

Hi @vappiah

HaplotypeCaller can perform adjustments to intervals by using -ip parameter. This parameter adds additional padding to supplied intervals therefore the tool can use a larger area covering the target interval. Other than this parameter HaplotypeCaller does not care about how bed file is generated.

If you think that you may be missing variants due to missing regions you may need to re run HaplotypeCaller and use -ip parameter to cover a larger region around your region of interest.

Regards.