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
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written
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maximilian.mayerhofer •
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
Thanks!
How do I specify the exclusion argument? Everything except Chr17?
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