Hello.
I have a question regarding the algorithm our lab uses for variant calling.
Essentially when calling the variants we call the variants for each chromosome individually. But this can cause errors (false positives) because if the reference map actually belongs to a different chromosome,say chromosome i, the algorithm will generate a score for the current chromosome having the variants called, say chromosome x.
However, for computational speed, splitting up the variant calling is more efficient because each node will do the process for each chromosome.
I am just looking for general advice.
The only way I can test this method is to finalize the VCF files, and use VCFtools to remove false positives.
-or I can use GATK, or Atlas2 to do a comparative analysis.
I have a question regarding the algorithm our lab uses for variant calling.
Essentially when calling the variants we call the variants for each chromosome individually. But this can cause errors (false positives) because if the reference map actually belongs to a different chromosome,say chromosome i, the algorithm will generate a score for the current chromosome having the variants called, say chromosome x.
However, for computational speed, splitting up the variant calling is more efficient because each node will do the process for each chromosome.
I am just looking for general advice.
The only way I can test this method is to finalize the VCF files, and use VCFtools to remove false positives.
-or I can use GATK, or Atlas2 to do a comparative analysis.
Comment