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Published 20 hours ago • verified publisher icon mroosmalen

NanoSV is not working

Open amrita1983 opened this issue 5 years ago • 1 comments

hi, I am trying to run NanoSV on my Nanopore data using the following command to generate the vcf file , but it ran for 2 weeks and no file was generated.

command used: NanoSV -t 5 -s /usr/bin/samtools -o /mnt/Diag/Nanopore_data_23_07_19/last-983/9_19.vcf /mnt/Diag/Nanopore_data_23_07_19/last-983/9_19_reads_sorted.bam this is giving the error Can't calculate coverage distribution. The bed file may be inappropriate for your bam file.

but if I am using the hg19.bed of my own as a bed file the file is not generating any output.

Please suggest me some solution so that I can run my nanopore bam to generate SVs.

amrita1983 avatar Sep 25 '19 08:09 amrita1983

Hi, How many lines (positions) are in your BED file?

jaesvi avatar Oct 02 '19 11:10 jaesvi