I am attempting to reanalyze some old data. Recently, an updated genome was released for the organism I work with. I had to map the reads to the new genome and what not. So what I have now is a bam file but now I want to do some variant calling so I can generate a vcf.
I know there is a lot of programs out there to do this but I am attempting to find the best one. I have tried using Platypus but the vcf file that it generates never contains any genome data. That is probably my fault but I can't seem to figure it out and there isn't much support. I tried VarDict but when I go to look at the vcf file, I get an error of "failure to parse tbx_vcf". I can really seem to find why I am getting that error. I have tried Freebayes and that has worked for me, but I have an issue with indels. Freebayes seems to call SNPs instead of acknowledging indels. I know there is GATK, but it seem like such a tedious piece of software. It looks like you have to go through 15 steps to just get anything worthwhile. I could be looking at the wrong examples. What I have notice about GATK is they try to make it so simple that it ends up just making things complicated.
Could anyone maybe give some suggestions or maybe some insight? Any help is very appreciated