Open mhjiang97 opened 8 months ago
I think a potential issue is that --mosaic tag. We refined parameters for --mosaic to only report SV with VAF 5-20%. So what you want to do is leading the --mosaic tag out since I see you have a heterozygous variant. I hope that makes sense . We are trying to make this more obvious and integrated , but for now mosaic and default mode address 5-20% VAF and 20+% VAF , respectively. If you ever want to debug on sniffles use --no-qc which writes out all the candidates. Thanks Fritz
if @mhjiang97 is using the --mosaic-include-germline tag will sniffles not report both SVs with AF 5-20% AND >20% ?
Yes, however we have received some reports that sometimes variants are missing, if that is the case for you please let us know
Hi!
I have a patient sample with a known gene fusion/genomic translocation (i.e. PAX5::ETV6). Sniffle 2.0.7 did call this BND in the vcf by running
sniffles --input mysample.bam --vcf out.vcf --non-germline --reference hg38.fa --tandem-repeats human_GRCh38_no_alt_analysis_set.trf.bed
:However, I cannot get similar results from Sniffles 2.2 by running:
sniffles --input mysample.bam --vcf out.vcf --mosaic --sample-id mysample --mosaic-af-max 0.5 --mosaic-af-min 0.01 --reference hg38.fa --tandem-repeats human_GRCh38_no_alt_analysis_set.trf.bed --mosaic-include-germline
In addition, I also tried to add the following flags but still got no BND indicating the known translocation:--bnd-min-split-length 500
,--qc-bnd-filter-strand False
,--bnd-min-split-length 1
,--cluster-merge-bnd 1500
Could you please advise me how to make sure the results of Sniffles 2.2 reliable? THANKS IN ADVANCE!
Best regards, Minghao