Comments (5)
Please attach you command for meth_phaser_parallel
, thanks
from methphaser.
Something along the lines of the following:
meth_phaser_parallel \
-b haplotagged.bam \
-r Mus_musculus.GRCm39.dna.primary_assembly.fa \
-g phased.gtf \
-vc output.phased.vcf \
-o output/ \
-t $SLURM_CPUS_PER_TASK
I did not get errors for the autosomes, sex chromosomes, and 3 other unlocalized genomic contigs. This is a minor issue for my purpose for now because if I had filtered the input .vcf for only autosomes this wouldn't have been an issue.
from methphaser.
Sorry, I have 0 knowledge about mouse datasets, but I would recommend only using MethPhaser on autosomes since random x inactivation. If you could give me more information on your dataset I might be able to look into it further. Additional helpful information could be reads, vcf, etc.. However, I recommend only using it on autosomes.
from methphaser.
Makes sense - thanks a lot!
from methphaser.
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 <module>
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 out of range
The command that I used was this one:
meth_phaser_parallel -t 10 -ml -2 \
-o methphaser \
-b grapevine.minimap2.filtered_only_primary.bam \
-r reference.fasta \
-g grapevine_phased.whatshap.stats.gtf \
-vc grapevine.clair3.phased.vcf.gz
Theoretically, I should not have problems with sex chromosomes, given the fact that grapevines do not possess them.
Thank you in advance for the help.
from methphaser.
Related Issues (14)
- Error when running meth_phaser_parallel HOT 3
- [E::bam_parse_basemod] MM tag refers to bases beyond sequence length HOT 17
- Duplicated and missing entries in .methphased.vcf HOT 6
- some block have only one SNP HOT 2
- Possible no caught error for single blocks
- Empty output vcf and bam HOT 4
- IndexError: list index out of range
- Question on secondary and supplementary reads HOT 4
- Two warning messages appear HOT 2
- The total size of the output bam file has decreased
- KeyError: ('C', 1, 'm') HOT 25
- No improved phasing HOT 5
- The command of Methphaser N50 HOT 4
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from methphaser.