Benchmarking

VariantAlignment object construction task for indels called by GATK4 HaplotypeCaller(4.0.2.1) for 75 whole-exome sequencing samples SJC-DS-1003 on a server with 32-core AMD EPYC 7542 CPU @2.90 GHz. pandas DataFrame used to store the indel calls.

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Tip

For genome-wide indel datasets, consider splitting your data into smaller chunks and analyzing them in parallel.