Madeline Couse
Madeline Couse
Hi @brentp, Is it possible for slivar to allow VEP's canonical flag in the CSQ field when exporting to tsv? E.g. gene_impact_transcript_Gene_CANONICAL_EXON_HGVSc_HGVSp_Protein_position_Consequence_PolyPhen_SIFT Thanks, Madeline
Hello, I am wondering why certain variants in the *annotation.csv file are not annotated with a heteroplasmic fraction. The same variants ARE annotated with a heteroplasmic fraction in the vcf....
Hello, I have noticed that when running LOFTEE, the LoF_flags are not being properly annotated; they are always blank in the output. So, for instance, rs201677741 from the ExAC vcf...
Hello, When I try to run enhanced insertion detection, I get an error message. This is my command: run_metasv.py --reference /mnt/data/GRCh37_bcgsc/GRCh37-lite.fa --boost_sc --sample A48018 --bam /mnt/data/A48018_2_lanes_dupsFlagged.bam --spades /home/hpcuser01/SPAdes-3.6.2-Linux/spades.py --age /home/hpcuser01/AGE/age_align...
It looks like metaSV ignores translocations in Lumpy vcf files. When I run metaSV, I get these messages ( a short sample): INFO 2016-10-28 11:30:02,622 metasv.main Load VCF files INFO...
Hello, There seems to be some bug in metaSV when the --boost_scs option is included. With this option, my deletion detection sensitivity drops dramatically from ~80% to 5% (as measured...
Hello, I've run MetaSV and received this following message: --- ERROR 2016-02-23 02:20:01,971 run_spades_single- Caught exception in worker thread Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/metasv/run_spades.py", line 75, in run_spades_single...