Bamstream and vcfconcat: tools for streamlining the joint-calling of genomic data

Bamstream and vcfconcat are specialized C++ tools designed to streamline genomic data processing. Bamstream consolidates short sequencing reads from multiple BAM files aligned to the same reference genome into a metadata-consistent multi-sample alignment stream, with a focus on efficient parallelization by operating on specific genomic regions. Vcfconcat resolves variation call conflicts in the overlapping ends of adjacent regions within gVCF files, prioritizing variants with higher quality scores to ensure accurate and consistent outputs for downstream analysis.