Damian
Damian
## Bug report Re-rerunning pipeline several times with option -resume causing that some tasks are processed again. For example the pipeline is finished, then I change something in the LAST...
Hey, are there any clear instructions how to run the software? After digging in Python files I built such command: `charger --input tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz --pathogenic-variant tests/examples/annotations/grch37_pathogenic_variants.vcf.gz --inheritance-gene-table tests/examples/annotations/inheritance_gene_table.tsv.gz --PP2-gene-list tests/examples/annotations/pp2_gene_list.txt.gz --clinvar-table...
Hey, after executing `plot-roh.py inputs/` I get error: ``` plot-roh.py inputs/ /usr/local/bin/plot-roh.py:432: UserWarning: Attempting to set identical left == right == 0 results in singular transformations; automatically expanding. ax1.set_xlim(min_x,max_x+xlim*max_x) Traceback...
Hey, is it possible to combine two types of the annotations? it would be helpful to draw this: https://eweitz.github.io/ideogram/annotations-overlaid and this: https://eweitz.github.io/ideogram/annotations-histogram on the same picture to make it more...
Hey, in .vcf there are many tags like this: chr1 924310 . C G 49 PASS **DP=5**;ADF=0,5;ADR=0,12;**AD=0,17**; GT:**DP**:ADF:ADR:**AD**:BSD:BSQ:ALFR 1/1:**5**:0,5:0,12:**0,17**:0,0,0,5,12,0,0,0:0,0,0,39,39,0,0,0:0.000,3.400 chr1 924321 . C G 58 PASS **DP=8**;ADF=0,8;ADR=0,13;**AD=0,21**; GT:**DP**:ADF:ADR:**AD**:BSD:BSQ:ALFR 1/1:**8**:0,8:0,13:**0,21**:0,0,0,8,13,0,0,0:0,0,0,38,39,0,0,0:0.000,2.625 chr10...
hey, I've noticed some inconsistency in Fred's metabarcoding [pipeline](https://github.com/frederic-mahe/swarm/wiki/Fred's-metabarcoding-pipeline) ``` # Discard sequences containing Ns, add expected error rates "${VSEARCH}" \ --quiet \ --fastq_filter "${TMP_FASTQ}" \ --fastq_maxns 0 \ --relabel_sha1...