I'm testing out samtools vs GATK for snp and indel calling, and looking at using pindel for SV in particular focusing on insertions and Delly for the other SV. What experience do people have of SNP calling and SV tools including filtering options?
Some possible discussion points: 1. Has anyone used Delly and found the results to be comparable with other SV detectors? 2. What filtering parameters do people use for SNP calling and indels?
I'm reading through papers on INDEL calling and samtools looks good for SNPs, GATK is better at small indels than samtools, but for larger INDELS and SV it doesn't seem as clear cut, I presume because it is a more complicated mechanism of detection.
Anybody got any recommendations of software they would use for a SNP/INDEL/SV calling pipeline. I've seen an older biostars post but there was no mention of larger indels and SV.