Dugé de Bernonville, Thomas

Hi all, using strobealign v0.7 and samtools v1.12, I ran the following lines: ``` $alignbin -t 4 $reffasta $forward $reverse | \ $samtoolsbin fixmate -u -m - - | \...

here is an example of a MISMATCH_MATE_CIGAR_STRING: output given by Picard ValidateSamFile: ``` ERROR::MISMATCH_MATE_CIGAR_STRING:Record 46, Read name A00604:215:HNL2GDSXY:2:2272:26576:36996, Mate CIGAR string does not match CIGAR string of mate ``` ```...

I am piping those following commands: ``` strobealign -t 4 $reffasta $forward $reverse | \ samtools fixmate -u -m - - | \ samtools addreplacerg -u -r "@RG\tID:${line}\tSM:${line}\tLB:Solution\tPL:illumina\tPU:none" - -...

regarding the `ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE `, Picard ValidateSamFile returns for example: ``` ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE:Record 2259, Read name A00604:215:HNL2GDSXY:2:1373:14136:8938, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ``` with...

Ok thanks for the anwser!

ok, seems that samtools command I add are introducing some confusing fields! I will try to troubleshoot the error I had with the Haplotypecaller because it seems to more a...

Many thanks for the reply and advices, much appreciated. I am working with 6 to 7 Kb RNA virus, I guess that should not be a problem. I will indeed...

Hi @Kuanhao-Chao, it seems that the installation also needs pytest. In addition, in the requirements, you should replace `parasail` by `parasail-python`. Congrats for the tool otherwise!

Ok this was because I added parasail by conda, not by pip. Below it the `yml` file I created for a capsule conda environment: ``` name: envLiftOn channels: - conda-forge...