Option to output realigned BAM file during --haplotypecaller step

[leonorpalmeira]

Hi,

elprep --haplotypecaller works extremely well and is very time efficient. We would like to start using it in our clinical setting for one of our projects which demands a very reduced turn-around time. However, we use a special feature of the original HaplotypeCaller called -bamout which outputs a BAM file with the realigned reads produced during the HaplotypeCaller step and which is not available in elprep5.

Would this be something that could be added to elprep?

Thanks a lot!
Leonor