I need to filter whatshap phased vcf before running NanoMethPhase?

vahidAK / NanoMethPhase

Methylation Phasing for Nanopore Sequencing

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I need to filter whatshap phased vcf before running NanoMethPhase? #25

Closed weishwu closed 5 months ago

weishwu commented 5 months ago

I used whatshap to phase my variants and the results contain both phased and unphased SNPs. My previous understanding based on the readme and some related posts was that I don't need to filter my VCF to select only phased SNPs for nanomethphase.py phase. However, when I tried using the filtered VCF I got different results. Is it true that I do need to do this filtering?

weishwu commented 5 months ago

Never mind. I checked the nanomethphase.py code. It does select only the lines with "1|0" or "0|1". I made a mistake in my test run which resulted in a different smoothing span parameter. I checked HP1_MethylFrequency.tsv and HP2_MethylFrequency.tsv which are the direct outputs of nanomethphase.py phase and they stay the same when I use the filtered vcf. Sorry for my ignorance.