paraphase

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test files

1

Hi - thanks for a great software! I'm trying to write a unit test, and I've borrowed your test files for smn1 HG00733_smn1_realigned.bam However, I cannot seem to run a...

MagdalenaZZ

add support for cram files

2

Hi, first of all, paraphase is a really good tool! It would be great if paraphase could accept cram files as input. Best, Florian

flokraft85

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....

gabeng

Paraphase determines output prefix from input filename

1

If the sample name isn't sanitized in the expected way (e.g., contains a `.`), the output names may be non-unique. For setting the prefix, I recommend determining the sample name...

williamrowell

Dealing with uneven coverage

3

Hello, Thank you for this great tool! I'm working with amplicon sequencing data capturing SMN gene. However, my data demonstrate uneven coverage along the SMN1 gene, which has resulted in...

keremozdel

How to determine some parameters in YAML files

1

Hi Dr. Chen, I'm curious about some of the settings in the [./data/38/config.yaml](https://github.com/PacificBiosciences/paraphase/blob/main/paraphase/data/38/config.yaml). Could you please tell me some of the details? Thank you! Taking Amy1A as an example ----------------------------------------------------------------------------------------...

evayfang2019

Exception: Two haplotypes are not equal length

2

File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/paraphase.py", line 146, in process_gene phaser_call = phaser.call()._asdict() File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/genes/rccx_phaser.py", line 438, in call ) = self.phase_haps(raw_read_haps) File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/phaser.py", line 1242, in phase_haps ass_haps, original_haps, hcn = hap_graph.run(debug=debug, make_plot=debug)...

liukeweiaway

Error index f8

4

Hi I am getting following error pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[faidx] Could not build fai index ../path/tmp/f8_ref.fa.fai\n' removing f8 from gene list works and I am using...

bioinfogit

Understanding CNV Distribution and Counts Across Haplotypes

5

I have recently begun studying CNVs (Copy Number Variations) and am utilizing the hg002 dataset for paraphase analysis. Upon comparing my paraphase results with the data available on your GitHub...

sloth-eat-pudding