search

mroosmalen / nanosv

SV caller for nanopore data
MIT License
90 stars 22 forks source link

what is an appropriate bed file? #74

Closed yekaizhou closed 2 years ago

yekaizhou commented 3 years ago

Hello,

I ran NanoSV like this: NanoSV -t 40 -o nanosv.vcf -b human_hg19.bed aln.bam, and it prompted The bed file may be inappropriate for your bam file.

The bed file is downloaded from your curation https://github.com/mroosmalen/nanosv/blob/master/nanosv/bedfiles/human_hg19.bed

The bam file is some ~8X ONT data downloaded from https://ftp.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/GM24385_1.fastq.gz, and then aligned to hs37d5, which can be perfectly ran on several other SV tools e.g. cuteSV, sniffles, svim.

I am wondering if I used NanoSV incorrectly and how can I adjust, and it seems to be the problem of the bed file. What I should do with the bed file?

kztyes commented 3 years ago

I also have this problem. Even if I use Samtools to generate a new bed file, it is still inappropriate for BAM files

fishercera commented 3 years ago

Bumping this.

I used bedtools to generate a random-spot BEDfile, after reading the scripts that are included to generate such. I did:

bedtools random -l 1 -seed 1938 -g Aedes_chr1.genome > Aedes_chrom1_randomspots.bed

Where "Aedes_chr1.genome" is just a two column file giving the length of Chromosome 1 -

1 310827022

I'm not sure if this is the right thing to do, but it has actually resulted in NanoSV giving me results, after 10 days of running...

Mrromeros commented 2 years ago

If you align your data to GRCH37, it will work with the default bed file they have, which is mislabeled hg19