DELLY CNV Calling

Question

[maximilian.mayerhofer]

So, I have to call CNVs of various bam-files using delly. Due to the rather low documentation, I am stuck.

I have a genomic reference file (Homo_sapiens.GRCh38.dna.chromosome.17.fa) as well as the ref-index file (.fa.fai), an input file (HG00512.CHS.sorted.bam) and bam-index (HG00512.CHS.sorted.bam.bai)

Since we only have to call CNVs on chromosome 17, the genomic reference is just the chromosome 17.

Input:

delly_cnv call -g Homo_sapiens.GRCh38.dna.chromosome.17.fa HG00512.CHS.sorted.bam

Output

BAM file chromosome chr1 is NOT present in your reference file Homo_sapiens.GRCh38.dna.chromosome.17.fa

I know, that Chr1 is not present in the reference - its just Chr17 Am I requested so specify that in some way?.

Best regards

Answer 1

[Pierre Lindenbaum]

don't change the fasta reference and use a BED with -x to exclude the orther contigs

-x [ --exclude ] arg              file with regions to exclude

[maximilian.mayerhofer]

Thanks!

How do I specify the exclusion argument? Everything except Chr17?

[trausch]

Yes, everything except Chr17. You can just list them all line-by-line:

chr1
chr2
...
chr16
chr18
chr19
...