Problem with Sniffles pipeline and SV calling help
1
0
Entering edit mode
6 weeks ago
njornet ▴ 20

I want to perform SV calling on nanopore data. From the resulting bam file after aligning and sorting I add the MD flag with samtools calmd and then run sniffles

sniffles -m alignment_md.bam -v SV_calls.vcf

Then when I want to sort the .vcf I get

FILTER 'STRANDBIAS' is not defined in the header

From what I've seen, the VCF is missing a FILTER option but I can't find how to choose the configuration for the missing filter. Anyway, I added it from someone asking another thing that happened to include this filter in their file:

##FILTER=<ID=STRANDBIAS,Description="VariantStrandBias < 0.02 && StrandBias > 0.02">

After doing that I'm able to sort the .vcf but I don't know how to interpret this. Is the a way to compare the called SVs with a database to see which of them are annotated similar to doing so with ClinVar for SNVs? Or should I just check if the called SVs correspond to the ones causing the diseases in my study?

SV sniffles StructuralVariant • 280 views
ADD COMMENT
0
Entering edit mode

From the resulting bam file after aligning and sorting

How was this done? MD tags should only be required if you did not align to a reference. Aligning with minimap2 followed by sorting should allow you to run sniffles on the sorted BAM.

ADD REPLY
2
Entering edit mode
6 weeks ago

After doing that I'm able to sort the .vcf but I don't know how to interpret this.

what is 'this' ? the broken VCF ? a description of the FILTER was missing in the header (bad workflow, programming error, etc...)

Is the a way to compare the called SVs with a database to see which of them are annotated similar to doing so with ClinVar for SNVs?

you could start with https://lbgi.fr/AnnotSV/

ADD COMMENT

Login before adding your answer.

Traffic: 2385 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6