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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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Incorrect position of BND in some cases #359

Open KoryukovMA opened 1 year ago

KoryukovMA commented 1 year ago

Hey! While working with our Nanopore data our goal was to use sniffles to extract BNDs annotate them using SnpEff and then design primers to verify some of them. But when we started extracting sequences from reference genome to construct primers we had some issues. Extracted sequences didn't align properly to read sequence. Then we saw that sniffles creates VCF file incorrectly (we assume it does). image You can see that bnd happened on chr1 2055695 and chr3 78882845. If we look at the bam file in IGV everything is fine with chr 1 position (since it shows that it was clipped from the right side [Right 443 soft]. image But if we go to chr 3 it shows that it was clipped on the opposite position from the one we have in our vcf file. image

If we understand everything correctly, sniffles output might contain only start positions of the read, but not the position where the actual BND event took place. It appears to be like that: image

Correct us if we are wrong

Best regards, MK

infotmatician commented 1 year ago

Hi, thank you for reporting this issue. Any updates @fritzsedlazeck ?

fritzsedlazeck commented 1 year ago

we didn t get to this yet.. sorry . Definitly high up the list. Fritz