xuchang116 / smcounter Goto Github PK

Hi!

Thanks for the great tool! I am wirking with QIAseq DNA panels and I am working using smCounter. However, all the variants that I am detecting are tagged at least as LSM. I am not quite sure what does this mean and what could be the problem of the samples. Example code:

python smCounter.py --outPrefix $i --bamFile "${i%}"_sorted.bam --bedTarget QIAseq_DNA_panel.CDHS-13593Z-900.roi.bed --mtDepth 3612 --rpb 8.6 --nCPU 10 --minBQ 20 --minMQ 30 --hpLen 10 --mismatchThr 6.0 --mtDrop 0 --maxMT 0 --primerDist 2 --threshold 0 --refGenome hg19.fasta --bedTandemRepeats simpleRepeat_hg19_smCounter.txt --bedRepeatMaskerSubset rmsk_hg19_smCounter_filter.txt --bedtoolsPath ..
/BEDTools/2.26.0/bin/ --runPath ./ --logFile $i

Any idea?
Thanks!

Hi, this is not an Error Report.
I was wondering, since we have regularly nearly 100 runs with smCounter, if it would be possible in any way to serialize the runs. Our computing power allows only one run per timepoint and not parralel. So preferable it would be to automatize: if run1 is finished then start run2 ....and so on.

Thank you in advance,
Edith

Hi,

I can't find the repository for smCounter2, and the link in the publication returns a 4054 (https://github.com/qiaseq/qiaseq-dna). Can you help me?

Wouter

Hi there, in addition to some of the dependencies mentioned in the README, could you please also mention the required/tested versions for pysam, scipy and Bedtools?
Thanks, Andreas