Question: INDEL detection tool recommendation
0
gravatar for nayshool
3.5 years ago by
nayshool20
Israel
nayshool20 wrote:

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?

cnv indel • 1.6k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by nayshool20

thanks everyone for your answers!

ADD REPLYlink written 3.5 years ago by nayshool20
3
gravatar for Brian Bushnell
3.5 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

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.

ADD COMMENTlink written 3.5 years ago by Brian Bushnell17k

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

Guess I need to upgrade.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax83k

Yep :)

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

ADD REPLYlink written 3.5 years ago by Brian Bushnell17k

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

ADD REPLYlink written 3.5 years ago by Ron990

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".

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Brian Bushnell17k

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

ADD REPLYlink written 21 months ago by ATpoint34k

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

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax83k

I mean the variant calling module.

ADD REPLYlink written 21 months ago by ATpoint34k
2
gravatar for Farbod
3.5 years ago by
Farbod3.3k
Toronto
Farbod3.3k wrote:

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

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Farbod3.3k
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