delly_error

[Manuela Sabatino]

Hi,

i need a support if it is possible!=)

i want to run delly software on a single chromosome, chr1, and I downloaded a chr1 fasta reference from https://www.ncbi.nlm.nih.gov/nuccore/CM000680.2?report=fasta

and i tried to run :

delly call -g hg19.chr1.fasta myfileinput.bam

where in file myfileinput.bam there is only the chr1 extracted  by means samtools from a larger bam file.

DELLY software doesn't run, but gives to me the error:

BAM file chromosome chrM is NOT present in your reference file hg19.chr1.fasta

I'm sure that in the used files the is only the chr1.

How could i fix the problem?

Thank in advance

Manuela

[tr]

Hi Manuela,

The chromosomes in your BAM file (samtools view -H  myfileinput.bam) need to match the genome FASTA file (grep ">" hg19.chr1.fasta). Sub-setting BAM files still keeps the original sequence dictionary so you need to reheader (samtools reheader ...) or use the original FASTA file used for alignment.

Best, Tobias