VCF output not reporting translocations/inversions/duplications

[damioresegun]

Hi,
I have used the command below to carry out a variant call with nanopore reads.
snakemake --snakefile /home/doresegu/scratch/apps/Tools/pipeline-structural-variation-2.0.2/Snakefile -p call --config input_fastq=/home/doresegu/scratch/private/Analysis/IsolatesToAssemble/sks047.fastq reference_fasta=/home/doresegu/scratch/private/PublicationAnal/NewGenomes/Cultured.fasta sample_name=sks047VsCultChecks --cores 32

This worked great and produced a VCF file however, I noticed that only insertions and deletions are reported. I looked in the cutesv_tmp.vcf which is the raw output of cuteSV to see that other SV forms were reported i.e. INV, TRA, DUP, BND.
So after some searching I managed to edit the Snakefile "filter_vcf" rule to include this:
sv_types = config.get("sv_type", "DEL INS TRA INV DUP"), as it only had DEL INS previously.
However this still didn't work. It appears that the filtering is happening with the bcftools view command:
bcftools view -i '(SVTYPE = "DEL" || SVTYPE = "INV" || SVTYPE = "DUP" || SVTYPE = "INS" ) && ABS(SVLEN) > 30 && ABS(SVLEN) < 100000 && INFO/RE >= 8' sks047VsCultChecks/sv_calls/sks047VsCultChecks_cutesv_tmp.vcf > sks047VsCultChecks/sv_calls/sks047VsCultChecks_cutesv_filtered_tmp.vcf

I can't find this command in the snakefile at all. So I manually carried out the bcftools command:
bcftools view -i '(SVTYPE = "DEL" || SVTYPE = "INV" || SVTYPE = "DUP" || SVTYPE = "INS" || SVTYPE = "TRA" || SVTYPE = "BND" ) && ABS(SVLEN) > 30 && ABS(SVLEN) < 100000 && INFO/RE >= 8' sks047VsCultChecks/sv_calls/sks047VsCultChecks_cutesv_tmp.vcf > sks047VsCultChecks/sv_calls/sks047VsCultChecks_cutesv_filtered_tmp.vcf
This still did not change anything however after removing the "INFO/RE >= 8" condition, I did see these forms in the output.

So my question is: where is the bftools command so that I can change it (to add more SVTYPEs) rather than having to manually carry out the filtration? I understand that the INFO/RE is dependent on mosdepth outputs so I won't need to change that. I just want to make sure it isn't missing forms that still fit within the thresholds.

[cjw85]

Hi @damioresegun

@philres should be able to confirm, but I believe that at the time of writing this piepline, cuteSV categorised events as only INS or DEL. We'll have to check whether this is the case for the latest version (if we are not using it already).

[damioresegun]

Ok thanks.
An update on my end: I have been able to see the different SVTYPEs are characterised in the raw cuteSV output though it is the read depth (of 8 in this case) that stops them from being called in the final variant file. So I guess the pipeline works as designed