Question: Local Assembly For Verification Of Indels
1
gravatar for lyfsa
8.0 years ago by
lyfsa30
lyfsa30 wrote:

Hi There,

I am trying to further verify indels detected from variant caller. For this, I extracted all the bam files reads, where indels were detected, run local assembly and realign the contigs from assembler back to reference to get the exact coordinates. My assumption is that, there should be gap in the regions where indels are detected. Can somebody provide an insight in this?

Thanks

local assembly • 2.4k views
ADD COMMENTlink modified 8.0 years ago by Jorge Amigo12k • written 8.0 years ago by lyfsa30
1
gravatar for JC
8.0 years ago by
JC11k
Mexico
JC11k wrote:

Actually, in my opinion, you are doing it right, I did the same sometime before with some Illumina paired-end data, I tested Velvet, ABySS and SOAPdenovo, when the region is small, all programs works perfectly, when you have a complex mix, ABySS can resolve better but SOAP produces longer contigs.

ADD COMMENTlink written 8.0 years ago by JC11k

Could you also tell me how velvet works for single end reads or unmapped reads in BAM files? I am quite skeptical about these reads.

ADD REPLYlink written 8.0 years ago by lyfsa30
1

the perfomance depends a lot in your library size, deep, quality and k-mer selected, so you gonna need many tries.

ADD REPLYlink written 8.0 years ago by JC11k

Thank you..you information is of great help...

ADD REPLYlink written 8.0 years ago by lyfsa30

After running the velvet and realigning them back to reference using mummer, I get several numbers of coordinates with 100% match with the ref sequence but I cannot make out long sequence out of that. I now have numbers of reads with many gaps in between. Can I say that if contig regions are overlapping with indels region, than those overlapping indels regions are false? or this is not the case. Sorry for asking so many questions but I would be grateful if you could help me.

ADD REPLYlink written 8.0 years ago by lyfsa30

as I said, the contig size and quality depends in many factor, try to change your kmer-size in velvet to see if you can get longer sequences

ADD REPLYlink written 8.0 years ago by JC11k
0
gravatar for Jorge Amigo
8.0 years ago by
Jorge Amigo12k
Santiago de Compostela, Spain
Jorge Amigo12k wrote:

one quick and easy way of checking this while comparing your variant calling results with a reference software would be to use GATK, since in the suggested pre-analysis steps it includes a local realignment one around indels. check its best practices page to have this process better described.

ADD COMMENTlink written 8.0 years ago by Jorge Amigo12k

I went through that link. But it looks like I cannot validate indels result from different caller??

ADD REPLYlink written 8.0 years ago by lyfsa30

my suggestion was either to use the full GATK pipeline described on the link above and compare the final variant calls with the previously obtained, or to use just the IndelRealign walker for your convenience, since it already provides local realignment of reads around indels detected and also around know indels you may provide (such as all known indels from 1000genomes, for instance).

ADD REPLYlink written 8.0 years ago by Jorge Amigo12k
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