Pierre Lindenbaum
Pierre Lindenbaum
you could you sam2tsv and check if there is a ALT variant carrying your variant. https://jvarkit.readthedocs.io/en/latest/Sam2Tsv/ or https://jvarkit.readthedocs.io/en/latest/Biostar322664/
Hi, VEP is detected using the standard field `CSQ=` not `VEP=` . See http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcf
the following annotations are expected: ANN= for SNPEFF, CSQ= for VEP, BCSQ for bcftools
@zhujiahua700403 Hi, it was not included in the 'big' jar because it's mostly unused and BreakDancer is pretty old, many SV caller outperform breakdancer now. You can alway download the...
hi, please try to increase the JVM memory using the -Xmx flag : ` java -Xmx10G -jar /opt/jvarkit/dist/jvarkit.jar biostar84452 ...`
cool thank you for the feedback
@JoseEspinosa unless I'm wrong differentalabundance doesn't work with the output of nf-atacseq . see https://nfcore.slack.com/archives/C045UNCS5R9/p1707383810019459?thread_ts=1707349504.512029&cid=C045UNCS5R9 > We had ambitions in this regard, but it hasn't been optimised for it yet,...
> I believe duplicate ALT alleles are allowed in VCF, hum , I don't think so. How would you know which ALT allele is associated to a genotype ?
I got the same bug, (and my email , full of dots, is in my path...). If fixed this on my side for paired-ends reads with the following code for...
@bentsherman it's sge