neusomatic

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Multi-patient training

2

I would like to run a large scale training task over thousands of labelled patient BAMs. Is this currently supported with neusomatic in any way, or will I have to...

chrissype

failed at the last step

23

example sample ran well, but when run with a pair of real data set, neusomatic failed at the last step with error: ### NeuSomatic stand-alone FAILED: Files ../example/work_standalone/NeuSomatic_standalone.vcf and ../NeuSomatic_standalone.vcf...

cbiitbian

OSError: [Errno 12] Cannot allocate memory

2

ERROR 2019-11-06 16:21:08,570 __main__ Aborting! ERROR 2019-11-06 16:21:08,598 __main__ preprocess.py failure on arguments: Namespace(dbsnp_to_filter=None, del_merge_min_af=0, del_min_af=0.05, ensemble_tsv=None, filter_duplicate=False, first_do_without_qual=False, good_ao=10, ins_merge_min_af=0, ins_min_af=0.05, long_read=False, matrix_base_pad=7, matrix_width=32, max_dp=100000, merge_r=0.5, min_ao=1, min_dp=5, min_ev_frac_per_col=0.06,...

jingmeng-bioinformatics

It takes several days to preprocess BAM files for testing

2

Hi Sayed, I started preprocessing the whole genome bam files (tumor and matched normal) for testing on my local computer (--number_threads 1) four days ago, and it has not finished...

jingmeng-bioinformatics

truth somatic variant .vcf file

3

hi: where can I get the `truth somatic variant .vcf file`? sincerely, Yueyang.

yueyangtime

Model training

1

Should I train a model every time I run a new project? Don’t you have a single model for Illumina reads like Deepvariant?

kokyriakidis

roger-liu-bina

Getting compilation error with latest codebase on Mac OS with gcc/g++ 9

1

``` In file included from /Users/siakhnin/tools/ont/neusomatic/neusomatic/include/bedio.hpp:8, from /Users/siakhnin/tools/ont/neusomatic/neusomatic/cpp/scan_alignments.cpp:31: /Users/siakhnin/tools/ont/neusomatic/neusomatic/include/Interval.hpp: At global scope: /Users/siakhnin/tools/ont/neusomatic/neusomatic/include/Interval.hpp:41:8: error: 'coverage' function with trailing return type has 'decltype(auto)' as its type rather than plain 'auto' 41...

yakneens

Hi, thanks for developing this great tool! I was able to use the pre-trained models in the [GitHub repository](https://github.com/bioinform/neusomatic?tab=readme-ov-file#trained-network-models) designed for short-read data. However, I have no luck in finding...

zhengzhenxian

Inputs for docker image Variant call ( --checkpoint )

2

Hi, I tested the tool with your test data bam bed, now i want to test on Long Read data of GIAB (PacBio/ONT) 1. I was wondering what is `--checkpoint`...

kiranpatil222