Michael Knudsen

I have noticed the same behavior and now routinely msisensor on dedupped BAMs (obtained using `samtools view -F 1024`). The results are then much closer to MSI status obtained by...

Marking duplicates is not sufficient. There is often a notable difference between using a BAM file with duplicates marked and with duplicates removed.

I am (unfortunately) able to reproduce the error using the bioconda version of SvABA: https://github.com/bioconda/bioconda-recipes/pull/16764 The complete build output can be seen here: https://circleci.com/gh/bioconda/bioconda-recipes/70026?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-checks-link I don't see anything suspicious regarding...

I had the same problem, and it went away after installing the `BSgenome.Hsapiens.UCSC.hg38` package. I think what it does is simply downloading all the stuff needing (including `chromInfo.txt.gz`) and placing...

Has anybody managed to run `v1.3.0` without getting a segmentation fault? If so, could you please share your conda environment using e.g. `conda env export`? I wonder if the problem...

> @micknudsen : Did you also use the refFlat.txt or a custom file for --annotations? @DanielAmsel Neither of these. I use a target BED file with gene names added as...