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Hello dear developers,
I will try PECAT for the first time for a diploid genome of about 500Mb and I am writing to ask for script recommendations. There are some template cfgfile files for some spe…
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Hi, may I ask a question: merqury provides phased block N50, it seems it does not provide phased block NG50, is it right or I missed something? Thanks in advance.
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/183) by Fong Chun Chan (Bitbucket: [Fong Chun Chan](https://bitbucket.org/Fong Chun Chan), ).**
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Hello,
I work with small marine animals and I have generated five single HiFi libraries from the same species. To avoid issues with the assemblies (heterozigosity, different haplotypes), I decided …
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Hi fellow,
Reading the unzip paper, it seems that the unzip has an strategy to phase the alternative haplotigs in a correct haplotype according to each other within a primary contig, right?
In o…
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Hi,
I am currently benchmarking tools that balance "compression and accessibility" for genotype data and encountered an issue when using XSI with large datasets. I hope you can assist me in resolvi…
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Hi,
The vcf file generated by longshot is giving error with whatshap phasing.
my command: whatshap phase --ignore-read-groups --reference Asm.pa_ctg.fasta Asm.pa_ctg_bwa_sorted_longshot.vcf.gz As…
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Hi Marcel,
I'm sorry for the additional issue, but I just wanted to ask if it was normal to have a significant number of unphased reads (specifically 99.99% of reads were unphased). I installed wha…
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There is some doubt about the phasing quality of the indels. In the image below, three different deletions are shown, and they overlap. When running HapCUT, it appears that these variants are phased t…
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Hi,
I wonder why some blocks are overlapped with other blocks. As shown in the tutorial, Block 1 is from SNP 1 to 89, and Block 2 is from SNP 1 to 955. Also, I ran the program with my own data, I …