INDEL detection tool recommendation

Question

[nayshool]

Hi guys,

I am looking for a tool to detect indels which range from couple of tens to couple of hundreds bases. What is the best tool for that mission?

thank you

Omri

BTW, what is the diffrence between CNV to an INDELs?

[nayshool]

thanks everyone for your answers!

Answer 1

[Brian Bushnell]

I recommend using BBMap for mapping reads and its variant-caller for calling variants:

bbmap.sh ref=ref.fa in=reads.fq.gz out=mapped.sam.gz maxindel=100k
callvariants.sh in=mapped.sam.gz ref=ref.fa vcf=variants.vcf ploidy=2

If you are using a very large genome like human you will probably want to add the flag "prefilter" to callvariants to reduce memory consumption.

Long deletions are fairly easy to detect, but it becomes harder to detect long insertions as they approach a significant fraction of the read length. So if you want to find long insertions, and you are using paired reads, you can increase the read length with BBMerge:

bbmerge.sh in=reads.fq outm=merged.fq outu=unmerged.fq rsem prefilter=2 k=62

Then map the merged and unmerged reads in two passes and feed both mapped files to CallVariants.

[GenoMax]

Hmm. Are vcf= and ref= new parameters in 36.6*+? I don't see them in 36.59.

Guess I need to upgrade.

[Brian Bushnell]

Yep :)

Actually, looks like ref= is undocumented; I'll fix that.

[Ron]

Hi Brian, Does BBMAP work on RNAseq data for variant calling?

[Brian Bushnell]

Yes, it does.

However, while BBMap is well-tested with RNA-seq data for mapping (and variant-calling, with a different variant caller), I have not tested CallVariants on RNA-seq data yet. The CallVariants includes a strand-bias test which you would probably want to disable because reads near the ends of transcripts will exhibit strong strand bias, as will anything with a stranded protocol.

To disable the strand bias test, add the flags "usebias=f minstrandratio=0".

[ATpoint]

Has your approach even been peer-reviewed and benchmarked by an independent group?

[GenoMax]

Not sure who this question is aimed at but bbmerge is published.

[ATpoint]

I mean the variant calling module.

Answer 2

[Farbod]

Dear Nayshool, Hi

Please have a look at Indel detection software tools, Tool For Finding Indel In Which Part Of Genes and This Paper for Comparison of SAMtools, PINDEL, PRISM and indelMINER .

And for BTW, please check this ResearchGate and NIH.

~ Best