We suggest using these resources to identify recommended workflows. Benchmarked results for SNP and indel detection are available from our accuracy page.
SNPs and indels are typically identified after the alignment of reads against a reference sequence.
The resulting aligned read data (typically in BAM format) are used as input and a variant call format (VCF) file is generated containing variant predictions against this reference sequence.
(For third-party tools, please see their GitHub pages for installation and usage. To address any issues with these and other third-party tools, please post to the Issues tab on the individual GitHub repositories as we cannot offer support for third-party software.)