Description
Hey there.
I use installed whamg via bioconda (Version: v1.7.0-311-g4e8c-dirty)
It worked well for one sample with a bam file as starting point after gatk4 workflow.
The other sample, however, stays for hours at "NFO: Gathering graphs from forest." and at some point, when i come back to work i just see that the run was killed. This is due to limited ram i guess since over the hours the ram is at around 95 percent and increases very slowly.
I use human data with the GRCh38 build.
The command:
whamg -x 4 -z -a ${REF} -f ${BAM} > vcf/${SAMPLE}/${SAMPLE}_whamg.vcf
I also tried to use "-c chr1,..." for get the main contigs, but this wouldn't work, even on a small test bam file because i still get variants in the end, which are not on the main contigs.
Interestingly, breakpoints are also calculated for non-main contigs "INFO: Number of putative breakpoints for: chrUn_JTFH01001929v1_decoy: 509"
I then tried to filter the bam file for the main contigs and then use that bam file and it still gets stuck in the Forest. Plus, despite having only main contigs in the bam file, the breaking points are calculated from all the contigs again, and it find breaking points.
I ran out of option and thus might exclude whamg to find structural variants unfortunately.
Any hints on what I can try?
Cheers