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I'm using `whatshap phase` to phase variants called from Nanopore sequencing data. I feel confused by some of the phasing results as the split reads do not appear to be consistent with the phased SNPs…
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I'm not sure whether `Whatshap` can be used to phase SVs. I tried it but some reads were not phased correctly. Ideally my reads should be phased into two haplotypes: one containing a ~5640bp insertion…
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Hi,
I want to co-phase SNVs and STRs.
I've placed the str VCF file as the --sv-file and longphase 'phase' manages to run and phase both VCFs.... BUT, because the STR VCF actually has one line per r…
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Hello,
I wonder how longphase handles supplementary alignments during phasing and haplotagging; as a separate read or they inherit HP/PS of the primary alignments.
Thank you,
Ayse
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With the addition of T6/S3 weapons the results view is starting to get less relevant for players that are still in the prebis, t4 and even (to some extent) T5.
If I am running Karazhan on an alt an…
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I'm of the opinion that all but SPIDEV should be phased out.
- MRAA isn't well maintained since Intel passed it on to the eclipse github org; contributions don't seem to be well verified/tested. And …
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After February 2023 kornia is phasing out jit support for some functions.
see [link](https://github.com/kornia/kornia/issues/2200)
If a jit error occurs anywhere, it is probably caused here.
Solu…
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### Ability name
Spectral
### Description
So far I havent read about it from anyone. As a filthy spec spammer I noticed that spec is way worse after the patch than before. The reason is not the pow…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/14) by me.**
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GATK outputs a PQ tag for each phased variant (except the first). We should do…
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Hi, i'm wondering whether the phasing of snv, sv and tr are consistent so that they can directly be concatenated? for example, if variants chr1_1_SNV1, chr1_100_SV1, and chr1_1000_TR1 all have genotyp…