problems genotyping, dysgu run --sites about dysgu HOT 3 CLOSED

Hi @warthmann,

The documentation is not very clear, apologies. When you filter against a normal sample, the calls returned should be unique to the mutant line. In theory this should mean all the sites in the normal are 0/0. In practise, some sites may have low support. When you supply a --sites file, the whole genome is analysed, not just the regions around the input sites. Any variant in the --sites file will make SV detection more sensitive around those sites, but all SVs from the genome will still be reported, which is consistent with your output.
I think the behaviour you were expected was a bit different - using dysgu to only re-genotype a file (rather than discovery as well). If you only want re-genotyping around the input sites, you can provide a bed file of regions to search using the --search option.
Hope that helps

from dysgu.

hello,
thank you for this clarification.
Regarding the --search flag in dysgu run. I can parse the required positions from the vcf. converting this into a .bed file, will I need to pad the positions in some way or can you recommend using the (same) position of the variant as BEGIN and END in the .bed? Alternatively, can I suggest including a feature similar to --all-sites for dysgu --filter? I.e., such that upon set flag dysgu --filter returns a vcf that also contains entries for a list of specified samples, or all samples for which a bam file is provided?
thanks a lot

from dysgu.

That is a good suggestion, I can try and add that in the next release.

In the meantime, you will need to parse the dysgu vcf to extract the regions surrounding each breakpoint. I recommend using pysam for this. The pad should be similar to the insert size: Pseudo code would be along the lines

import pysam

vcf = pysam.VariantFile('dysgu.vcf')
outbed = open('out.bed', 'w')
insert = 200

for v in vcf.fetch():
    outbed.write(f"{v.chrom}\t{v.pos - insert}\t{v.pos + insert}\n")
    if r.info['SVTYPE'] != 'TRA':
        outbed.write(f"{v.chrom}\t{v.end - insert}\t{v.end + insert}\n")
    else:
        outbed.write(f"{v.info['CHR']}\t{v.info['CHR2_POS'] - insert}\t{v.info['CHR2_POS'] + insert}\n")

Dysgu will sort and merge intervals as needed.

from dysgu.