Re: Delly output VCF filteration criteria

[NGS lab]

Hi guys,

any body can help me regarding DELLY VCF filtering criteria, how to find good SV or BND.

What are are the important parameter we shall look to find out SV quickly.

Thank you In advance.

Rajesh K Maurya

INDIA

[Damian Loska]

I'd be happy to know the filtering criteria too.
delly filter -f germline
is a very general command, however I'd like to be able to filter manually files directly from the command:
delly call -g hg38.fa -o s1.bcf -x hg38.excl sample1.bam

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[Damian Loska]

any help with that?
So using only a base command, to a single file (no batch processing):

delly call -g ref.fa -x human.hg38.excl.tsv test.bam -o delly.raw.test.bcf

How to filter delly.raw.test.bcf?

What threshold to which INFO or SAMPLE should I use?

[Damian Loska]

ChatGPT and DeepSeek propose such filters:
bcftools filter -i 'INFO/PE > 4 & INFO/SR > 3 & FMT/GQ > 20 & QUAL > 200 & FMT/GT!="0/0" & FILTER="PASS"' -o samp.vcf $dellybcf

Why nobody answer this topic?

[Tobias Rausch]

I think I disagree with ChatGPT here because delly calls small SVs that will lack PE support but also repeat-mediated SVs that potentially lack SR support. Filtering for PASS and non-ref. genotypes makes sense, of course and then QUAL>200 (or >300 or >500), depending on how stringent you want to filter.

To view this discussion visit https://groups.google.com/d/msgid/delly-users/37dd4cb6-86a9-4f1c-927a-232e9cfd88fan%40googlegroups.com.

[Damian Loska]

Great, thanks for the hint!!!