methphaser

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Two warning messages appear

2

Two warning messages appear when i run _meth_phaser_parallel_ : ``` warning: /home/lixin/miniconda3/envs/viaenv/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import require ``` and ``` /home/lixin/miniconda3/envs/viaenv/lib/python3.9/site-packages/scipy/__init__.py:155: UserWarning:...

XLeeHIT

The total size of the bam file outputted by methphaser has decreased. My bam size after Whatshap processing is 175 G, but the total size of the bam after methphaser...

XLeeHIT

Empty output vcf and bam

4

Hi, I am using methphaser as a singularity image on an HPC. I have made the singularity image work with the test data, so shouldn't be any technical issues with...

andosl

Hi. I am getting the same error: ``` Traceback (most recent call last): File "/iga/scripts/dev_modules/mambaforge/envs/duet-v0.6/bin/methphasing", line 1471, in main(sys.argv[1:]) File "/iga/scripts/dev_modules/mambaforge/envs/duet-v0.6/bin/methphasing", line 1396, in main [0], phased_region_list[1][0])] IndexError: list index...

Mar10L

Hello there, I just wanted to report what I think is a small error: ``` /home/sivico/mambaforge/envs/Phasing/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import require Traceback...

sivico26

Duplicated and missing entries in .methphased.vcf

6

When I look at the entries in the output `.methphased.vcf`, there seems to be complete duplicate rows (not just that one variant is methphased into different haplotypes and therefore split...

liuy0421

No improved phasing

5

Hi, We are trying to phase a region, but there remains a gap which cannot be phased using SNPs. Now we have tried the high-accuracy and high-success parameters of MethPhaser,...

JesseBNL

KeyError: ('C', 1, 'm')

32

hello， I got an error when I used mathphaser： /share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future...

Wshengquan

The command of Methphaser N50

4

We noticed that your N50 is different from Whatshap N50, and the Methphaser N50 is more reasonable. Could you please provide a command to call the N50 calculation method in...

Humonex

This resolved #9 on our in-house dataset. I hope that someone could test on the other dataset.

shka