delly_v1.1.6 cnv failed

dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

BSD 3-Clause "New" or "Revised" License

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delly_v1.1.6 cnv failed #326

Open lmanchon opened 1 year ago

lmanchon commented 1 year ago

--Hi,

i run this command:

ref_fasta=GRCh38_p13.fa map_file=Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz

delly_v1.1.6 cnv -u -z 1000 -i 90000 -b my.bed -o my.bcf -c my.cov.gz -g ${ref_fasta} -m ${map_file} my.bam

and it failed with: Scanning Windows Please increase the window size. Coverage is too low!

by how much should I increase the window size ?

thank you --

tobiasrausch commented 1 year ago

Usually 10-fold increases are a good start

delly cnv -i 10000 -j 10000 -w 10000 ...

then

delly cnv -i 100000 -j 100000 -w 100000 ...

...

oceancongliu commented 6 months ago

Hi, I met a error, ~/biosoftware/delly_v1.2.6_linux_x86_64bit cnv -g genome.fasta -m map.fa.bgz -l N1A10.bcf -o N1A10.cnv.bcf N1A10.sort.markdup.bam [2024-Mar-31 20:39:56] delly cnv -g genome.fasta -m N1A10.map.fa.bgz - l N1A10.bcf -o N1A10.cnv.bcf N1A10.sort.markdup.bam [2024-Mar-31 20:40:03] Scanning Windows Segmentation fault (core dumped).

Can you give me some advices? Thanks.