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Hi,
I have a few questions related to the phasing options.
1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) > 0.05:"? If I have tumor data …
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Hi @hannespetur,
Sorry I might have missed this somewhere. Does Graphtyper perform SNV discovery from PacBio or Nanopore data or is this something still under development?
Thank you
Kind reg…
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Requested in #311 by @jcgrenier:
> Another useful QC that could be integrated would be one using Genotyping array data. As sometimes we like to do analysis like eQTL analysis and use both genotypin…
ewels updated
3 years ago
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Hello --
Thank you for developing and maintaining a powerful resource for the genomics community.
I've genotyped SVs for a species of bird, and noticed there was an aberrantly large inversion t…
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I am trying to run ```g2gtools extract``` with a g2gtools DB created from a GTF and a FASTA. It is running successfully but after 14 minutes it stops:
`2024-08-05T19:38:02.180415541Z GTTCCAATACTGTG…
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Is there a way to specify the -r option per read? My samples are a mix of pacbio and nanopore reads. I was guessing the SV and SNP genotyping would be more accurate if I called on the whole population…
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We are interested in describing rates of migration among genetically similar populations. Given that they are genetically similar, we would expect to falsely identify some individuals as migrants. W…
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There were 31 of the 104 SNPs in the JSON file that didn't have a "*relative_values.--" entry. Would those 31 have 0 missing calls?
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Hi,
I m trying to impute HLA in TopMed Imputed data using Michigan Imputation Server. However job fails stating "**Calculating QC Statistics failed**". Also, when I try to impute Michigan Server Impu…
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We would like to verify whether there is a significant difference in efficiency of the hm pipeline for seq GWAS.
1. Calculate the average % of dropped and unable to harmonise variants among a repres…
ljwh2 updated
4 months ago