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?
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written
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richardc.gsc •
2 answers
Speaking of INDEL callers, Scalpel was extensively benchmarked in this below paper, showing high accuracy (especially for large indels).
Accurate de novo and transmitted indel detection in exome-capture data using microassembly
Also, we highlighted the use of Scalpel to reduce errors in whole-genome and whole-exome studies in a follow-up paper.
Reducing INDEL calling errors in whole genome and exome sequencing data
Feel free to check out Scalpel - my go-to caller for indels :)
Scalpel is available here: http://scalpel.sourceforge.net/
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hanfang.cshl •
I typically use VarScan to call SNPs and small indels
I also noticed this algorithm was recently published, but I haven't really found small indels to be problem. Larger indels are tricker (for that, I've found CoNIFER to be the best option for exome-capture data, but I think there is still room for improvement).
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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?