Ben Liesfeld

Bioconda atropos package tied to python 3.6

1

Do you have an idea why the bioconda package is tied to python 3.6? I am trying to track down conda dependency issues and this may be one of them....

Next release?

10

Hi, a few changes have accumulated on the master branch that would be very helpful. Are there any plans for a release in the near future?

paraphase output VCFs cannot be parsed by htslib tools

4

Tools that rely on `htslib` like `IGV` and `GATK` return errors when loading `VCF` files generated by `paraphase 3.0 0`. The example is HG001. [HG001_CBS_variants.vcf.gz](https://github.com/PacificBiosciences/paraphase/files/14233209/HG001_CBS_variants.vcf.gz) ### IGV ``` WARNING [Feb....

VarSim generated readnames too long for SAM/BAM

2

VarSim may generate read names that cannot be written into SAM or BAM format. `bwa-mem` fails to perform alignment on these reads. ``` chr13_31453404_33401170-1248109-,chr13_31453404_33401170-1248192-I,chr13_31453404_33401170-1248107-,chr13_31453404_33401170-1248218-D,chr13_31453404_33401170-1248109-:chr13_31453404_33401170-1248218-D-,chr13_31453404_33401170-1248217--:::::::::::622992MjYyMDg=:0 ``` `samtools import` can be used...

Hi, first of all, the public docker image is highly appreciated! I just noticed that it does not contain the python environment to run scripts like `generate_small_test_ref.py`. I had to...

Large expansions without reads covering the entire repeat region

4

Hi, Thank you for this great tool and for diligently answering questions here. If I understand correctly, TRGT only considers reads in the analysis that span the entire repeat region....