schmutzi
schmutzi copied to clipboard
grenaud
Maximum a posteriori estimate of contamination for ancient samples
Good afternoon Gabriel. I have been experiencing some problems obtaining the contamination estimates. I have mitogenomes from ancient human samples sequenced paired-end 2x75. I have two cases with questions: A)...
Hi, Thanks for the great tool. I am trying to compile on Mac OSX M2 (apple silicon) and recieve the following error: `gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003)...
Hello, this is very good software. Thanks to you for developing it. However, I have a question, and I hope to get your help. As the principle of your software,...
Hi, I am aware this is an issue caused by not producing a proper calmd bam, but maybe you have some ideas? I ran the calmd file without any issues...
Hi Gabriel, I'm trying to run schmutzi.pl and I am getting the following error: ``` running cmd endoCaller -seq b07_npred_1_endo.fa -log b07_npred_1_endo.log -name MT -qual 0 -logindel 50 -deamread -deam5p...
I was able to succesfully run schmutzi.pl on some samples, unfortunately i get an unusual error with some. Error: Cannot parse the contamination output file = [sample_name]_1_mtcont.out What does it...
Hello! I have been having some problems using schmutzi when using rescaled BAM files vs just deduplicated BAM files (identical in terms of other processing steps like adapter trimming, merging,...
Hello, I am currently planning estimating contamination for non-UDG NEBNext® Ultra™ II DNA library kits. As you see, non-UDG NEBNext® Ultra™ II DNA library kits have different damage patterns: They...
