User: jeff.hammerbacher

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Curious

Posts by jeff.hammerbacher

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Comment: C: Compendium of validated somatic variant calls with associated reads and referenc
... Thanks for the thoughts Cyriac! I've been building a spreadsheet of BAMs and MAFs from the TCGA papers that claim to have performed validation manually and was hoping someone else had already done this work, because I am lazy. I'm unhappy with forming a gold set from the union of calls from other ca ...
written 2.5 years ago by jeff.hammerbacher90
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Compendium of validated somatic variant calls with associated reads and reference?
... We're working on a new somatic variant caller and could use some validated somatic variant calls to ensure our software is working well. We're working to compile a list of validated somatic variant calls together with the raw or aligned tumor and normal reads that were used to generate the variant c ...
variant calling tcga cancer written 2.5 years ago by jeff.hammerbacher90 • updated 2.5 years ago by Cyriac Kandoth4.6k
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Answer: A: Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
... Our lab recently released PyEnsembl to work with Ensembl data locally. We also wrote a blog post with some information on how to use the library. ...
written 2.5 years ago by jeff.hammerbacher90
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Answer: A: How To Control Wgsim Base Qualities?
... I forked wgsim and made the quality score configurable using the -Q command line argument. I've made I the default value for the quality score (Phred quality score of 40). Feel free to use my fork at https://github.com/hammer/wgsim to alleviate the need for the post-processing step with awk. Previo ...
written 4.4 years ago by jeff.hammerbacher90
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Why Are Some 23Andme Snp Ids Prefixed With "I" Instead Of "Rs"?
... I understand that "rs" is short for Reference SNP. What does the "i" prefix mean, and where can I learn more about this namespace for SNPs? ...
mitochondria snp written 4.5 years ago by jeff.hammerbacher90 • updated 2.9 years ago by Andrius Bubelis0
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Comment: C: 23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One
... Thanks! FYI, I found the locations of the PAR regions for the 23andMe reference genome at ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p10/par.txt ...
written 4.5 years ago by jeff.hammerbacher90
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23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One
... I've downloaded my raw data from 23andMe. I'm a male. For most loci on the X chromosome, there is a single base in the "genotype" column. However, at the beginning and end of the chromosome, for a few hundred loci, there are two bases in the "genotype" column. I've looked at my wife's 23andMe data, ...
written 4.6 years ago by jeff.hammerbacher90 • updated 4.6 years ago by Pierre Lindenbaum96k

Latest awards to jeff.hammerbacher

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Why Are Some 23Andme Snp Ids Prefixed With "I" Instead Of "Rs"?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Why Are Some 23Andme Snp Ids Prefixed With "I" Instead Of "Rs"?

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