ngmlr and sniffles applied to de novo assembly about sniffles HOT 3 CLOSED

Dear Sangjin Lee,
I think that is a clever way.
So with the 90x coverage you can find often artifacts that simply accumulate. They will likely be marked as IMPRECISE and often have a genotype of 0/0 indicating a very low support or frequency of reads supporting them. The AF= tag gives you the allele frequency of each event.
Without knowing your sample I assume you will find alot of false insertion and translocation calls.
Translocation can indicate some evidence that some contigs/scaffolds could further be joined.
Insertions accumulate sometimes due to a base calling error/ polymerase stuttering during the sequencing. PacBio is working on it and it should get improved over the next version of the basecaller.

0/1 SVs can happen as these are the heterozygous SVs. As you know most of the assemblers only report one sequence as a representation.

So what I would do is to focus on the 1/1. These should either mark problems from NGMLR+ sniffles or form the assembly. You might want to pinpoint these regions and also look at the short read evidence for these regions.

I hope this is helping you. Otherwise feel free to ping me and we can chat.
Cheers
Fritz

from sniffles.

Hey Fritz,

Thank you for the swift response. This is a really helpful response. I would love to be able to discuss this further with you, but I would to do so in private as the data is unpublished. If there are any additional problems, can I send you an email through your baylor college of medicine email address?

I will concentrate on the homozygous genotypes for now, visualize the long-read bam file and short-read bam file using IGV. I guess I could potentially increase the number of minimum reads required for genotyping to reduce the number of false positive variants.

Best,
Sangjin Lee

from sniffles.

Yes feel free to ping me. The fastest is over my gmail: [email protected] ,but the bcm also works.

I think it would be great to stick the heads together and come up with a small pipeline that can automatically assess this. Just an idea, but I am happy to discuss further options.
Cheers
Fritz

from sniffles.