Table 1.
Feature comparison of variant detection and annotation pipelines
| Features | VDAP-GUI | SPANDx | WEP | fastq2vcf | ngs_backbone | SeqGene | GAMES | CLCBio |
|---|---|---|---|---|---|---|---|---|
| Web-based/Stand-alone | Stand-alone | Stand-alone | Web-based | Stand-alone | Stand-alone | Stand-alone | Stand-alone | Web-based/stand-alone |
| Free for academic use | Yes | Yes | Yes (restricted access) | Yes | Yes | Yes | Yes | No |
| GUI | Yes | No | Yes | No | No | No | No | Yes |
| Organisms | No restriction | No restriction | Human | No restriction | No restriction | No restriction | No restriction | No restriction |
| Platforms supported | Illumina/454/ion torrent | Illumina/454/ion torrent | Illumina | Multiple | Multiple | Multiple | Multiple | Illumina/454/ion torrent |
| Mixed platform support | Yes | No | No | Yes | No | No | No | Yes |
| Paired-end support (PE) | Yes (PE for Illumina) | Yes (PE for Illumina) | Yes | Yes | Yes | Yes | Yes | Yes |
| Quality control | Yes | No | Yes | Yes | Yes | Yes | No | Yes |
| Sequence trimming | Yes (Default/Custom) | No | Yes | No | Yes | No | No | Yes (Default/Custom) |
| WGS | Yes | Yes | No | Yes | No | No | Yes | Yes |
| WES | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes |
| RNA-seq | No | No | No | No | Yes | Yes | No | Yes |
| Tools for variant call | SAMtools/VarScan/Freebayes | SAMtools/GATK | GATK | SAMtools/GATK/SNVer | SAMtools/GATK | SeqGene SNP pileup | GAMES method | Proprietry method |
| Variant types | SNP/INDEL | SNP/INDEL | SNP/INDEL | SNP/INDEL | SNP/INDEL | SNP/INDEL/CNV | SNP/INDEL/CNV | SNP/INDEL/CNV |
| Annotation | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes, limited |
| Reports | Yes | No | Yes | Yes (limited) | Yes (limited) | Yes (limited) | Yes | Yes |