Hi all, I'm wondering which tools people are using for Illumina whole genome indel calling. I'm specifically interested in finding indels that are shorter than a read length. While we use other tools for somatic (tumour-normal) calling, what I'm most interested in here are tools that work on just one sample at a time.
Currently we are using Samtools mpileup to generate the SNPs and INDELS all at once. What other tools should I consider?
I have tried GATK, Pindel and Dindel. All of them are great.
I am trying to run scalpel 0.5.2, discovery-mode, on a simple bam file of ~300 MB size. The scalpel-discovery runs fine, but it ends up creating a variants.indel.vcf file with only headers and no content in it.
Here is the command that I used
I am wondering if @hanfang.cshl may have any insights?