take so long time on chr1

[DayTimeMouse]

Hi,

I used VolcanoSV to call variants, but it has been stuck on chr1 for more than four days. The program has not reported any errors, and appears that hifiasm is still running. Is this normal?

path_to_volcanosv='../VolcanoSV'
for i in {1..22}
do
echo "***********************assembly for chr${i}*******************"
python3 ${path_to_volcanosv}/bin/VolcanoSV-asm/volcanosv-asm.py \
-bam hifi_tumor.bam \
-o volcanosv_asm_output_tumor \
-ref genome.fa \
-t 20 \
-chr ${i} \
-dtype Hifi \
-px tumor \
-asm hifiasm
done

Best regards.

[volcano1998]

Thank you for trying out our tool!

It is strange because In my experiment chr1 takes less than 2 days. How big is your BAM file?

[DayTimeMouse]

The size of BAM file is 88.12GB.

Now, the process is moving on.

Another question, I'd like to call somatic SVs using paired tumor and normal samples. However, VolcanoSV can only process one sample at a time. So, should I use surviour to select the SVs that are only included in the tumor sample?

[volcano1998]

I'm glad to hear it move foreward. Yes, you need to get VCF file for normal and tumor independently, then run survivor to get the somatic SVs.

[DayTimeMouse]

Thanks!

I would like to ask when VolcanoSV is expected to support mutation detection on chrX and chrY?

[volcano1998]

Sorry for not highlighting it in the readme. VolcanoSV is designed only for autosome chromosomes. I just added this to the readme.