snps
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apriha
tools for reading, writing, merging, and remapping SNPs
Hi, Is it possible to use this package to only parse specific chromosome(s) or region(s), provided the input VCF is tabix indexed? At the moment, I am running `tabix --print-header...
The mapmygenome file has additional column GC.score, that gives the confidence level of the SNP. It will be good to filer out SNP rows that has lower confidence (say <...
Integrate @changlubio's [GenomePrep](https://github.com/changlubio/GenomePrep/) capability to identify and filter low quality SNPs for a SNP array that are "not statistically plausible" based on analysis of [1000 Genomes Project](https://www.internationalgenome.org) data. Requires resolution...
Integrate @changlubio's [GenomePrep](https://github.com/changlubio/GenomePrep/) capability to identify one of the five primary SNP array clusters for DTC results. Reference: C. Lu, B. Greshake Tzovaras, J. Gough, A survey of direct-to-consumer genotype...
Simplifies `Reader` and `Writer` classes. Adds class-based parsers (fixes #119).
Currently, for file types that use a generic parser, their source is identified as "generic". Suggest changing the source to "unknown".
I'm using aws ec2 ubuntu. It does not allow me to create an individual. >>> user662 = l.create_individual('User662', '/home/ubuntu/myprojectdir/AaronAzuma.zip') Traceback (most recent call last): File "", line 1, in File...
When deduplicating sex chromosomes is a useful thing to do. However, in some conditions the default methods of sex detection can give incorrect results e.g. when homozygous reference alleles are...
Currently, there is a single general Reader class with various methods for different sources. I wonder if a series of specific classes for different filetypes be better e.g. Reader23andMe, ReaderAncestry,...