sambamba-markdup: Read reference ID is out of range This only happens for some (one at the moment) bam file. Others work fine. v0.6.1 command: sambamba_v0.6.1 markdup -t 8 merged.bam merged_markdup.bam complete
sambamba 0.6.8 from bioconda I run markdup on a cluster and generated the segmentation fault error and left a core.* temporary file. This error is consistent among all the computer with different CPU (either Xeon or AMD Opteron). Any thoughts?
samtools fixmate -m namesort.bam fixmate.bam -m不能少 3) Markdup needs position order samtools sort -o positionsort.bam fixmate.bam 4) Finally mark duplicates samtools markdup positionsort.bam markdup.bam 二、sambamba markdup的使用 一行命令即可: sambamba markdup--overflow-list-size600000--tmpdi...
Description of bug In file sambamba/sambamba.py line 93: https://github.com/ewels/MultiQC/blob/45ce9ae0160c38e250e3e0e4a9335adc5af26b6b/multiqc/modules/sambamba/markdup.py#L93 A simple try/except should do it. May want to check every pla...