Comments (4)
Hi Andreas,
I would imagine this is an issue related to the read length or incomplete reference genome. I have only run MethPhaser before with the standard human genome reference like GRCh37 or GRCh38, which is not like the FASTA reference that you provided.
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Hi Fu-Yilei,
Thanks a lot for speedy answer!
I reformatted all the input files replacing "contig_1" with "chr13", and I reindexed the bam, fasta, and vcf files. This seemingly did the trick (?!). I have to evaluate the output and will let you know.
Regards,
Andreas
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Thanks, if this is the case there might be some chromosome name reading bug in MethPhaser, I will look into it and make it workable when the chromosome name is something other than "chrxx"
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Hi,
It seems it is the "contig_1" in these files that makes MethPhaser struggle. This is the only change that I can do to the files to make them work. But it is an easy trick, not a big deal.
Would be great to discuss some of the outputs with you. When I open the haplotagged bam in IGV, the methylation pattern seems quite similar on the two haplotypes and it is hard to eyeball why MethPhaser has chosen one haplotype from the other.
Kind regards,
Andreas
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Related Issues (11)
- IndexError: list index out of range HOT 5
- Duplicated and missing entries in .methphased.vcf HOT 6
- some block have only one SNP HOT 2
- Possible no caught error for single blocks
- 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
- Error when running meth_phaser_parallel HOT 3
- [E::bam_parse_basemod] MM tag refers to bases beyond sequence length HOT 17
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