How can I compare my CLC denovo variants against BWA+samtools variants?

Question

[k.kathirvel93]

Dear all, How can I compare my CLC denovo assembly variants against with BWA+samtools variants. Thanks in advance.

[Benn]

Maybe try a Venn Diagram?

[k.kathirvel93]

Dear b.nota Thank you so much for your reply, but am asking about visualisation comparison.....

[Benn]

What do you exactly mean with 'visualisation comparison'? Can you give an example?

[k.kathirvel93]

Means I got many variants from both Denovo and BWA. I have used mauve to visualise variants for Denovo and IGV for BWA (i have used samtools for variant calling). From BWA i got a vcf file and I opened it in IGV. The prob is I cannot compare those variants, coz variants are appearing in a different position in both tools. If i get a vcf file from Denovo assembly it is possible to open both files in IGV. but its impossible from my knowledge. any suggestion.....

[h.mon]

Did you apply any quality filters to avoid spurious SNPs? And please, update your question, describing what you did in more detail.

[GenoMax]

Bring the BWA+Samtools variants in as a track into CLC and then use "compare variants" tools found under "resequencing analysis".

Answer 1

[h.mon]

Export both as .vcf (I guess the BWA+SAMtools should already be a vcf file) and open both on IGV, along with your reference genome.

[k.kathirvel93]

Mr.h.mon Actually the problem is I have used PGAP pangenome analysis tool to find the variants from DeNovo assembly...from PGAP output i cannot get any vcf files. Which means i can't convert PGAP outputs into vcf format. that is a main problem.any suggestion ...........

[k.kathirvel93]

Mr. H.mon first I did CLC denovo assembly with my 5 diff strains genome sequences, then annotation done by RAST, then i have used PGAP pangenome analysis to find SNP variants. then in other side i did BWA alignment with that same 5 strains with reference genome, Here i have used samtools for variant calling. Finally i got some number of variants from both of the tools..Now i want to compare those varaints which i got from Denovo and BWA....That's it........

[Benn]

I think your problem is that you use different reference genomes for each analysis. Now you try to compare apples with oranges...

Try to do the analysis with 1 reference, that will make live much easier.

[k.kathirvel93]

No, I have used same Reference only....for both PA01 Pseudomonas genome......

[Benn]

Well maybe PGAP pangenome analysis is not suitable for your research question (I don't know for sure, I have never used it).

I think it could help if you align (also with BWA) your de novo assembled contigs to the reference genome and do the same variant analysis with samtools.

See e.g., this post: Compare A Denovo Assembly To The Reference Genome