VCF file filter for breakpoints

Question

[EpiExplorer]

Hi,

I am trying to filter VCF file and extract breakpoints. Does anyone know how to do it using bcftools?

I have extracted SV calls using sniffles with the BAM file I had after long read sequencing. Now I would like to use bcftools to extract the regions that show translocations and breakpoints. How do I filter these regions and then how do I utilize that filtered region list for visualization using IGV?

Thanks for your help and time!

[prasundutta87]

Hi,

The breakpoints for SV calls are generally the start and end coordinates (POS and END). For extracting this information, you can use bcftools query-https://samtools.github.io/bcftools/howtos/query.html

You can limit your search to only translocations using -i or include, for example -i '"SVTYPE="TRA"' You should also keep the chromosome information from the CHROM column to account for interchromosomal translocation events.

Then you can easily put the start and end coodinates (along with chromosome number/name) in IGV to visualise the translocation event. You may need to keep soft-clipping ON in IGV in order to visualise the event.

[EpiExplorer]

Hi Prasun,

Thanks for your response. I tried the following command but still doesnt work. I get an error Missing the --format option. The Command used is below: bcftools query --include SVTYPE="TRA" SV_calls_OGM.vcf -o output.txt
Thanks.

[prasundutta87]

You need to add -f

for example

bcftools query --include 'SVTYPE="TRA"' -f "%CHROM\t%POS\t%END\n"  SV_calls_OGM.vcf -o output.txt

Play around with it using examples from the link I shared.