Error in ReadInBams (GenomicRanges::seqnames(target))

[alejandroriglesias]

Hello:

I am running DECoN in Windows, but we are having a lot of errors in the execution of ReadInBams.bat. This is the error:
"Error in GenomicRanges::seqnames(target) : error in evaluating the argument 'x' in selecting a method for function 'seqnames': Error: object target not found"

Our inputs are the BAM files, the .bed file (without the "chr" prefix, due to previous errors we eliminated the prefix) and the reference fasta file in .fa format. We cannot find a solution for this, so if anybody had this error or knows how to solve it, we would very much appreciate it.

[shethharsh08]

Hi Alejandro

I am facing similar issues with running the code. How did you manage to remove chr prefix from BAM file?

Cheers!

[alejandroriglesias]

Hi:
We ended up running DECoN in an Linux machine and the chr prefix problem dissapeared.

[shethharsh08]

Hi Alejandro
Thanks for the prompt response. I am running the script in Ubuntu 18.04 LTS machine and I am getting this issue. Briefly, FASTQ files were aligned against human_g1k_v37.fasta human genome and variant calling was carried out using GATK v4. Any help would be greatly appreciated!
Cheers